Sat Mar 15 09:34:09 UTC 2025 I: starting to build spades/unstable/amd64 on jenkins on '2025-03-15 09:34' Sat Mar 15 09:34:09 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_33/52944/console.log Sat Mar 15 09:34:09 UTC 2025 I: Downloading source for unstable/spades=4.0.0+dfsg1-2 --2025-03-15 09:34:09-- http://deb.debian.org/debian/pool/main/s/spades/spades_4.0.0%2bdfsg1-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2546 (2.5K) [text/prs.lines.tag] Saving to: ‘spades_4.0.0+dfsg1-2.dsc’ 0K .. 100% 398M=0s 2025-03-15 09:34:09 (398 MB/s) - ‘spades_4.0.0+dfsg1-2.dsc’ saved [2546/2546] Sat Mar 15 09:34:09 UTC 2025 I: spades_4.0.0+dfsg1-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: spades Binary: spades Architecture: amd64 Version: 4.0.0+dfsg1-2 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Sascha Steinbiss , Michael R. Crusoe , Alexandre Mestiashvili , Étienne Mollier Homepage: https://github.com/ablab/spades Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/spades Vcs-Git: https://salsa.debian.org/med-team/spades.git Testsuite: autopkgtest Testsuite-Triggers: bwa Build-Depends: debhelper-compat (= 13), dh-sequence-python3, asciidoctor, clang-format, clang-tidy, clang-tools, cmake, libbam-dev, libbamtools-dev, libbz2-dev, libboost-thread-dev, libc++-dev, libcuckoo-dev, libgtest-dev, libhts-dev, libnlopt-dev, libnlopt-cxx-dev, libparallel-hashmap-dev, libspoa-dev, libssw-dev, libxxhash-dev, libzstd-dev, llvm-dev, lynx, python3-all, python3-joblib, python3-yaml, zlib1g-dev Package-List: spades deb science optional arch=amd64 Checksums-Sha1: feda8783c3544227edbe3537798411d570095b6a 9961224 spades_4.0.0+dfsg1.orig.tar.xz daf32e9ce26ef92fdcd5b93c5c2d3cb1089e7d43 48644 spades_4.0.0+dfsg1-2.debian.tar.xz Checksums-Sha256: b3634165e29be26856f0ccaa1bac5b140747d744419b475ffea0a7f1df4e7a5a 9961224 spades_4.0.0+dfsg1.orig.tar.xz 1e4056b330d0e3a429474d5df0e96fc3d1250a3561cb7a4e7450b3c34810cfc6 48644 spades_4.0.0+dfsg1-2.debian.tar.xz Files: 962bfd8677abfde9ee7856f048ea06a6 9961224 spades_4.0.0+dfsg1.orig.tar.xz 5c18169ff811179cd874851d21234f7b 48644 spades_4.0.0+dfsg1-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmexyr0RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFB1Q/7BgocyqSPmVBuwCgKJFIZFi9rVn02kxXj geGU1SVyDjCnz1X0Zg9uScQIEyhusEKMjrae1x42QE60e20L4IdDK5gB3r5ONHYU 5F9AHch3amwpwTCoknd9tMIkO8Z1ziLnDGmffdwJ8F5g/EFjo5LKMIt6gtG+ru+P xDJ4lM4DWIp8YZyVGo6tSVtqzIhsLM3IfUaFC8MvuWx1BoJG5oDQQO7i9Sz5oZYu x+rUfUmPen+Qb8nXDpygbNZusFVHNkfgeWr6OyPGezXZWDFE+xc6UMrreHQ2nGVN 408T9GF351uhmgKwlUOH89FpIyz+NswzZL51tNtyclguKfLwlv5drWxHc2awqIje MEY5NxDMf2WhO0L7UgSa7HBekck70/vNTi5elnpplBaZR5gvHluelQ+lAjGvUYEq xVjgpwgSAupRMUUGSgqKEfklZI0MGnR7Jf7Fpulvg8VmSVeS1E61GRHFzh8PyQY8 RJADAu4ifUsoTsT/3NB74TtDtULvdn4wphKRF7Y2wALPkEEtgCg3m86Ck18Y4AoT jdv4cAN3qTd4wQkA/Vff1xYfIPmqjTQ6dn96EXA45NsXjaU6FA/0ArnbKO7LooAs uQXKUuQ0c51rRRvhQixBth4/+n9HMxekiXjtJ0iKVo5w2JZt0inL8yWh3Ghr+l2N oPHWctX69X8= =K5Ti -----END PGP SIGNATURE----- Sat Mar 15 09:34:09 UTC 2025 I: Checking whether the package is not for us Sat Mar 15 09:34:09 UTC 2025 I: Starting 1st build on remote node infom01-amd64.debian.net. Sat Mar 15 09:34:09 UTC 2025 I: Preparing to do remote build '1' on infom01-amd64.debian.net. Sat Mar 15 09:47:27 UTC 2025 I: Deleting $TMPDIR on infom01-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Mar 14 21:34:16 -12 2025 I: pbuilder-time-stamp: 1742031256 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [spades_4.0.0+dfsg1-2.dsc] I: copying [./spades_4.0.0+dfsg1.orig.tar.xz] I: copying [./spades_4.0.0+dfsg1-2.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./spades_4.0.0+dfsg1-2.dsc: unsupported subcommand dpkg-source: info: extracting spades in spades-4.0.0+dfsg1 dpkg-source: info: unpacking spades_4.0.0+dfsg1.orig.tar.xz dpkg-source: info: unpacking spades_4.0.0+dfsg1-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 0002_use_debian_packaged_python-joblib.patch dpkg-source: info: applying 0101_cmake_ignore_removed_python-yaml.patch dpkg-source: info: applying 0102_cmake_ignore_removed_python-joblib.patch dpkg-source: info: applying bamtools-cmake.patch dpkg-source: info: applying 0114_use_debian_provided_libs.patch dpkg-source: info: applying 0118_adjust_spades_home_again.patch dpkg-source: info: applying fix-bool-cast dpkg-source: info: applying python3.patch dpkg-source: info: applying yaml_load.patch dpkg-source: info: applying debuginfo.patch dpkg-source: info: applying debian_bwa_zlib.patch dpkg-source: info: applying workdir_for_test.patch dpkg-source: info: applying disable_local_convertutf.patch dpkg-source: info: applying typos.patch dpkg-source: info: applying use_debian_xxhash.patch dpkg-source: info: applying use_debian_cuckoo.patch dpkg-source: info: applying samtools_missing_source.patch dpkg-source: info: applying deactivate_tests_with_no_data.patch dpkg-source: info: applying raw_regex_pattern.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3120234/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='1565885f97cb48118c92303f54f3c060' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='3120234' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.EDGLKHX8/pbuilderrc_BGe8 --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.EDGLKHX8/b1 --logfile b1/build.log spades_4.0.0+dfsg1-2.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom01-amd64 6.1.0-31-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3120234/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, asciidoctor, clang-format, clang-tidy, clang-tools, cmake, libbam-dev, libbamtools-dev, libbz2-dev, libboost-thread-dev, libc++-dev, libcuckoo-dev, libgtest-dev, libhts-dev, libnlopt-dev, libnlopt-cxx-dev, libparallel-hashmap-dev, libspoa-dev, libssw-dev, libxxhash-dev, libzstd-dev, llvm-dev, lynx, python3-all, python3-joblib, python3-yaml, zlib1g-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19785 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on asciidoctor; however: Package asciidoctor is not installed. pbuilder-satisfydepends-dummy depends on clang-format; however: Package clang-format is not installed. pbuilder-satisfydepends-dummy depends on clang-tidy; however: Package clang-tidy is not installed. pbuilder-satisfydepends-dummy depends on clang-tools; however: Package clang-tools is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on libbam-dev; however: Package libbam-dev is not installed. pbuilder-satisfydepends-dummy depends on libbamtools-dev; however: Package libbamtools-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-thread-dev; however: Package libboost-thread-dev is not installed. pbuilder-satisfydepends-dummy depends on libc++-dev; however: Package libc++-dev is not installed. pbuilder-satisfydepends-dummy depends on libcuckoo-dev; however: Package libcuckoo-dev is not installed. pbuilder-satisfydepends-dummy depends on libgtest-dev; however: Package libgtest-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on libnlopt-dev; however: Package libnlopt-dev is not installed. pbuilder-satisfydepends-dummy depends on libnlopt-cxx-dev; however: Package libnlopt-cxx-dev is not installed. pbuilder-satisfydepends-dummy depends on libparallel-hashmap-dev; however: Package libparallel-hashmap-dev is not installed. pbuilder-satisfydepends-dummy depends on libspoa-dev; however: Package libspoa-dev is not installed. pbuilder-satisfydepends-dummy depends on libssw-dev; however: Package libssw-dev is not installed. pbuilder-satisfydepends-dummy depends on libxxhash-dev; however: Package libxxhash-dev is not installed. pbuilder-satisfydepends-dummy depends on libzstd-dev; however: Package libzstd-dev is not installed. pbuilder-satisfydepends-dummy depends on llvm-dev; however: Package llvm-dev is not installed. pbuilder-satisfydepends-dummy depends on lynx; however: Package lynx is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-joblib; however: Package python3-joblib is not installed. pbuilder-satisfydepends-dummy depends on python3-yaml; however: Package python3-yaml is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: asciidoctor{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} clang-19{a} clang-format{a} clang-format-19{a} clang-tidy{a} clang-tidy-19{a} clang-tools{a} clang-tools-19{a} cmake{a} cmake-data{a} comerr-dev{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} googletest{a} groff-base{a} icu-devtools{a} intltool-debian{a} krb5-multidev{a} libarchive-zip-perl{a} libarchive13t64{a} libbam-dev{a} libbamtools-dev{a} libbamtools2.5.2{a} libboost-atomic1.83-dev{a} libboost-atomic1.83.0{a} libboost-chrono1.83-dev{a} libboost-chrono1.83.0t64{a} libboost-date-time1.83-dev{a} libboost-date-time1.83.0{a} libboost-serialization1.83-dev{a} libboost-serialization1.83.0{a} libboost-system1.83-dev{a} libboost-system1.83.0{a} libboost-thread-dev{a} libboost-thread1.83-dev{a} libboost-thread1.83.0{a} libboost1.83-dev{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libc++-19-dev{a} libc++-dev{a} libc++1-19{a} libc++abi-19-dev{a} libc++abi1-19{a} libcereal-dev{a} libclang-common-19-dev{a} libclang-cpp19{a} libclang1-19{a} libcom-err2{a} libcuckoo-dev{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libcurl4t64{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libedit2{a} libelf1t64{a} libevent-2.1-7t64{a} libexpat1{a} libffi-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgc1{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libgtest-dev{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu-dev{a} libicu76{a} libidn2-0{a} libidn2-dev{a} libjsoncpp26{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} libldap-dev{a} libldap2{a} libllvm19{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libncurses-dev{a} libncurses6{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libnlopt-cxx-dev{a} libnlopt-cxx0{a} libnlopt-dev{a} libnlopt0{a} libobjc-14-dev{a} libobjc4{a} libp11-kit-dev{a} libp11-kit0{a} libparallel-hashmap-dev{a} libpfm4{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl-dev{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} librhash1{a} librtmp-dev{a} librtmp1{a} libruby{a} libruby3.3{a} libsasl2-2{a} libsasl2-modules-db{a} libspoa-dev{a} libspoa7.0.0{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libssw-dev{a} libssw0{a} libtasn1-6{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libunistring5{a} libunwind-19{a} libunwind-19-dev{a} libuv1t64{a} libxml2{a} libxml2-dev{a} libxxhash-dev{a} libyaml-0-2{a} libz3-4{a} libz3-dev{a} libzstd-dev{a} llvm{a} llvm-19{a} llvm-19-dev{a} llvm-19-linker-tools{a} llvm-19-runtime{a} llvm-19-tools{a} llvm-dev{a} llvm-runtime{a} lynx{a} lynx-common{a} m4{a} man-db{a} media-types{a} netbase{a} nettle-dev{a} openssl{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} python3{a} python3-all{a} python3-joblib{a} python3-minimal{a} python3-pygments{a} python3-yaml{a} python3.13{a} python3.13-minimal{a} rake{a} rapidjson-dev{a} readline-common{a} ruby{a} ruby-asciidoctor{a} ruby-did-you-mean{a} ruby-minitest{a} ruby-net-telnet{a} ruby-power-assert{a} ruby-rubygems{a} ruby-test-unit{a} ruby-webrick{a} ruby-xmlrpc{a} ruby3.3{a} rubygems-integration{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: binfmt-support bzip2-doc fonts-lato krb5-locales libarchive-cpio-perl libclang-rt-19-dev libgpm2 libjs-jquery libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc linux-sysctl-defaults mailcap psmisc publicsuffix python3-numpy python3-psutil python3-pytest ruby-sdbm systemd zip 0 packages upgraded, 213 newly installed, 0 to remove and 0 not upgraded. Need to get 237 MB of archives. After unpacking 1344 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.2-2 [859 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.0-1 [107 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.2-2 [2210 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.2-2 [27.1 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 13.0.0 [29.3 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025a-2 [259 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.2-2 [1952 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.2-2 [746 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.1 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.2-2 [28.1 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-7 [64.9 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-7 [878 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.4.1-1 [1427 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20241223 [164 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-2 [337 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-2 [109 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-2 [43.5 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-5 [92.4 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 rubygems-integration all 1.19 [5488 B] Get: 30 http://deb.debian.org/debian unstable/main amd64 rake all 13.2.1-1 [65.2 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 ruby-did-you-mean all 1.6.3-2 [20.9 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 ruby-minitest all 5.25.4-2 [66.2 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 ruby-power-assert all 2.0.3-1 [11.8 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 ruby-test-unit all 3.6.2-1 [79.1 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 ruby-webrick all 1.9.1-1 [59.6 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 ruby-xmlrpc all 0.3.3-2 [24.4 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-2 [52.5 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libruby3.3 amd64 3.3.7-1 [6274 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 ruby3.3 amd64 3.3.7-1 [827 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libruby amd64 1:3.3+b1 [5440 B] Get: 42 http://deb.debian.org/debian unstable/main amd64 ruby-rubygems all 3.6.3-1 [406 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 ruby amd64 1:3.3+b1 [6560 B] Get: 44 http://deb.debian.org/debian unstable/main amd64 ruby-asciidoctor all 2.0.23-1 [214 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 asciidoctor all 2.0.23-1 [88.7 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-7 [294 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-3 [862 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libicu76 amd64 76.1-3 [9721 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.3+b1 [699 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libllvm19 amd64 1:19.1.7-3 [26.0 MB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libclang-cpp19 amd64 1:19.1.7-3 [13.2 MB] Get: 57 http://deb.debian.org/debian unstable/main amd64 libgc1 amd64 1:8.2.8-1 [247 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libobjc4 amd64 14.2.0-18 [43.3 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libobjc-14-dev amd64 14.2.0-18 [172 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libclang-common-19-dev amd64 1:19.1.7-3 [740 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 llvm-19-linker-tools amd64 1:19.1.7-3 [1260 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libclang1-19 amd64 1:19.1.7-3 [7638 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 clang-19 amd64 1:19.1.7-3 [116 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 clang-format-19 amd64 1:19.1.7-3 [92.7 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 clang-format amd64 1:19.0-63 [6352 B] Get: 66 http://deb.debian.org/debian unstable/main amd64 clang-tools-19 amd64 1:19.1.7-3 [8961 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 python3-yaml amd64 6.0.2-1+b2 [136 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 clang-tidy-19 amd64 1:19.1.7-3 [1883 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 clang-tidy amd64 1:19.0-63 [6116 B] Get: 70 http://deb.debian.org/debian unstable/main amd64 clang-tools amd64 1:19.0-63 [6164 B] Get: 71 http://deb.debian.org/debian unstable/main amd64 cmake-data all 3.31.6-1 [2268 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.4-1.1 [349 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 78 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-2 [109 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.9+dfsg-2 [194 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.12.1-3 [369 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 librhash1 amd64 1.4.5-1 [132 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.50.0-2 [154 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 cmake amd64 3.31.6-1 [12.0 MB] Get: 98 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.2-1 [55.7 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 105 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20250308 [115 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 googletest all 1.16.0-1 [517 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 icu-devtools amd64 76.1-3 [215 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.21.3-5 [60.0 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.21.3-5 [42.5 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.21.3-5 [42.6 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.21.3-5 [54.2 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.21.3-5 [126 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libbam-dev amd64 0.1.19+dfsg-6 [118 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libbamtools2.5.2 amd64 2.5.2+dfsg-6+b1 [161 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libbamtools-dev amd64 2.5.2+dfsg-6+b1 [222 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libboost1.83-dev amd64 1.83.0-4.1+b2 [10.6 MB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libboost-atomic1.83.0 amd64 1.83.0-4.1+b2 [234 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libboost-atomic1.83-dev amd64 1.83.0-4.1+b2 [236 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 libboost-chrono1.83.0t64 amd64 1.83.0-4.1+b2 [240 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libboost-chrono1.83-dev amd64 1.83.0-4.1+b2 [246 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libboost-date-time1.83.0 amd64 1.83.0-4.1+b2 [230 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libboost-serialization1.83.0 amd64 1.83.0-4.1+b2 [334 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libboost-serialization1.83-dev amd64 1.83.0-4.1+b2 [373 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 libboost-date-time1.83-dev amd64 1.83.0-4.1+b2 [240 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 libboost-system1.83.0 amd64 1.83.0-4.1+b2 [231 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 libboost-system1.83-dev amd64 1.83.0-4.1+b2 [232 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 libboost-thread1.83.0 amd64 1.83.0-4.1+b2 [269 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 libboost-thread1.83-dev amd64 1.83.0-4.1+b2 [277 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libboost-thread-dev amd64 1.83.0.2+b2 [3624 B] Get: 137 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b7 [316 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 libunwind-19 amd64 1:19.1.7-3 [62.9 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 libc++abi1-19 amd64 1:19.1.7-3 [105 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 libc++1-19 amd64 1:19.1.7-3 [303 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 libc++abi-19-dev amd64 1:19.1.7-3 [128 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 libunwind-19-dev amd64 1:19.1.7-3 [81.6 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 libc++-19-dev amd64 1:19.1.7-3 [1286 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 libc++-dev amd64 1:19.0-63 [6056 B] Get: 146 http://deb.debian.org/debian unstable/main amd64 rapidjson-dev all 1.1.0+dfsg2-7.3 [98.0 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 libcereal-dev amd64 1.3.2+dfsg-5 [221 kB] Get: 148 http://deb.debian.org/debian unstable/main amd64 libcuckoo-dev all 0.3.1-3 [37.5 kB] Get: 149 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.11.0-1 [131 kB] Get: 150 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.11.0-1 [29.3 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.12.1-3 [365 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 153 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.22.0-1+b1 [598 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.9-2 [455 kB] Get: 155 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.9-2 [455 kB] Get: 156 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.8-2 [103 kB] Get: 157 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB] Get: 158 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.20.0-2 [99.2 kB] Get: 159 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-3 [329 kB] Get: 160 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-3 [642 kB] Get: 161 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10.1-1 [1318 kB] Get: 162 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.9-2 [1401 kB] Get: 163 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.21.3-5 [16.1 kB] Get: 164 http://deb.debian.org/debian unstable/main amd64 libldap-dev amd64 2.6.9+dfsg-2 [311 kB] Get: 165 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 166 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 167 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 168 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.64.0-1 [115 kB] Get: 169 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.8.0-1 [91.3 kB] Get: 170 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.11.0-1 [34.0 kB] Get: 171 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.11.0-1 [179 kB] Get: 172 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get: 173 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB] Get: 174 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.4.1-1 [2787 kB] Get: 175 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get: 176 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.7+dfsg-1 [371 kB] Get: 177 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.12.1-3 [480 kB] Get: 178 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB] Get: 179 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.23-1+b1 [56.0 kB] Get: 180 http://deb.debian.org/debian unstable/main amd64 libffi-dev amd64 3.4.7-1 [60.8 kB] Get: 181 http://deb.debian.org/debian unstable/main amd64 libgtest-dev amd64 1.16.0-1 [259 kB] Get: 182 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get: 183 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.21+ds-1 [463 kB] Get: 184 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.6.4-1 [323 kB] Get: 185 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.21+ds-1 [1733 kB] Get: 186 http://deb.debian.org/debian unstable/main amd64 libicu-dev amd64 76.1-3 [10.8 MB] Get: 187 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5+20250216-2 [105 kB] Get: 188 http://deb.debian.org/debian unstable/main amd64 libncurses-dev amd64 6.5+20250216-2 [353 kB] Get: 189 http://deb.debian.org/debian unstable/main amd64 libnlopt0 amd64 2.7.1-6+b4 [178 kB] Get: 190 http://deb.debian.org/debian unstable/main amd64 libnlopt-dev amd64 2.7.1-6+b4 [46.8 kB] Get: 191 http://deb.debian.org/debian unstable/main amd64 libnlopt-cxx0 amd64 2.7.1-6+b4 [205 kB] Get: 192 http://deb.debian.org/debian unstable/main amd64 libnlopt-cxx-dev amd64 2.7.1-6+b4 [13.5 kB] Get: 193 http://deb.debian.org/debian unstable/main amd64 libparallel-hashmap-dev all 1.4.1+ds-1 [205 kB] Get: 194 http://deb.debian.org/debian unstable/main amd64 libpfm4 amd64 4.13.0+git83-g91970fe-1 [368 kB] Get: 195 http://deb.debian.org/debian unstable/main amd64 libspoa7.0.0 amd64 4.1.4-2+b1 [74.1 kB] Get: 196 http://deb.debian.org/debian unstable/main amd64 libspoa-dev amd64 4.1.4-2+b1 [9808 B] Get: 197 http://deb.debian.org/debian unstable/main amd64 libssw0 amd64 1.1-15+b2 [21.8 kB] Get: 198 http://deb.debian.org/debian unstable/main amd64 libssw-dev amd64 1.1-15+b2 [24.6 kB] Get: 199 http://deb.debian.org/debian unstable/main amd64 libxml2-dev amd64 2.12.7+dfsg+really2.9.14-0.3+b1 [794 kB] Get: 200 http://deb.debian.org/debian unstable/main amd64 libxxhash-dev amd64 0.8.3-2 [81.0 kB] Get: 201 http://deb.debian.org/debian unstable/main amd64 libz3-dev amd64 4.13.3-1 [107 kB] Get: 202 http://deb.debian.org/debian unstable/main amd64 llvm-19-runtime amd64 1:19.1.7-3 [551 kB] Get: 203 http://deb.debian.org/debian unstable/main amd64 llvm-runtime amd64 1:19.0-63 [5904 B] Get: 204 http://deb.debian.org/debian unstable/main amd64 llvm-19 amd64 1:19.1.7-3 [16.4 MB] Get: 205 http://deb.debian.org/debian unstable/main amd64 llvm amd64 1:19.0-63 [8328 B] Get: 206 http://deb.debian.org/debian unstable/main amd64 python3-pygments all 2.18.0+dfsg-2 [836 kB] Get: 207 http://deb.debian.org/debian unstable/main amd64 llvm-19-tools amd64 1:19.1.7-3 [511 kB] Get: 208 http://deb.debian.org/debian unstable/main amd64 llvm-19-dev amd64 1:19.1.7-3 [43.1 MB] Get: 209 http://deb.debian.org/debian unstable/main amd64 llvm-dev amd64 1:19.0-63 [6152 B] Get: 210 http://deb.debian.org/debian unstable/main amd64 lynx-common all 2.9.2-1 [1193 kB] Get: 211 http://deb.debian.org/debian unstable/main amd64 lynx amd64 2.9.2-1 [641 kB] Get: 212 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.13.2-2 [1044 B] Get: 213 http://deb.debian.org/debian unstable/main amd64 python3-joblib all 1.4.2-3 [216 kB] Fetched 237 MB in 11s (22.0 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19785 files and directories currently installed.) Preparing to unpack .../libpython3.13-minimal_3.13.2-2_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.2-2) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.7.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.7.0-1) ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.2-2_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.2-2) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.2-2_amd64.deb ... Unpacking python3.13 (3.13.2-2) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/spades-4.0.0+dfsg1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../spades_4.0.0+dfsg1-2_source.changes dpkg-buildpackage: info: source package spades dpkg-buildpackage: info: source version 4.0.0+dfsg1-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=src --buildsystem=cmake debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1' dh_auto_clean find . -name "*.pyc" -delete rm -rf /build/reproducible-path/spades-4.0.0+dfsg1/debian/man_src/*.html /build/reproducible-path/spades-4.0.0+dfsg1/debian/man_src/*.? rm -rf /build/reproducible-path/spades-4.0.0+dfsg1/debian/man make[1]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1' dh_autoreconf_clean -O--sourcedirectory=src -O--buildsystem=cmake debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1' dh_clean -X.orig make[1]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1' debian/rules binary dh binary --sourcedirectory=src --buildsystem=cmake dh_update_autotools_config -O--sourcedirectory=src -O--buildsystem=cmake dh_autoreconf -O--sourcedirectory=src -O--buildsystem=cmake debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1' dh_auto_configure -- -DBoost_NO_BOOST_CMAKE=TRUE -DSPADES_BOOST_ROOT:PATH="/usr" cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DBoost_NO_BOOST_CMAKE=TRUE -DSPADES_BOOST_ROOT:PATH=/usr ../src -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found bamtools: /usr/lib/x86_64-linux-gnu/libbamtools.so -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") found components: CXX -- Found BZip2: /usr/lib/x86_64-linux-gnu/libbz2.so (found version "1.0.8") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found -- Looking for wsyncup in /usr/lib/x86_64-linux-gnu/libncurses.so -- Looking for wsyncup in /usr/lib/x86_64-linux-gnu/libncurses.so - found -- Looking for wsyncup in /usr/lib/x86_64-linux-gnu/libcurses.so -- Looking for wsyncup in /usr/lib/x86_64-linux-gnu/libcurses.so - found CMake Warning (dev) at cmake/deps.cmake:29 (find_package): Policy CMP0144 is not set: find_package uses upper-case _ROOT variables. Run "cmake --help-policy CMP0144" for policy details. Use the cmake_policy command to set the policy and suppress this warning. CMake variable BOOST_ROOT is set to: SPADES_BOOST_ROOT For compatibility, find_package is ignoring the variable, but code in a .cmake module might still use it. Call Stack (most recent call first): CMakeLists.txt:66 (include) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake/deps.cmake:29 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): CMakeLists.txt:66 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost: /usr/include (found version "1.83.0") Making Release Configuration... -- Building SPAdes version 4.0.0 Building SPAdes from N/A, sha: N/A CMake Deprecation Warning at /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- -- Override standard malloc (MI_OVERRIDE=ON) -- Enable abort() calls on memory allocation failure (MI_XMALLOC=ON) -- Enable printing of error and warning messages by default (MI_SHOW_ERRORS=ON) -- Use the C++ compiler to compile (MI_USE_CXX=ON) -- -- Library base name: mimalloc -- Version : 2.0 -- Build type : none -- C++ Compiler : /usr/bin/c++ -- Compiler flags : -Wall;-Wextra;-Wno-unknown-pragmas;-fvisibility=hidden;-ftls-model=initial-exec;-fno-builtin-malloc -- Compiler defines : MI_XMALLOC=1;MI_SHOW_ERRORS=1 -- Link libraries : /usr/lib/x86_64-linux-gnu/libpthread.a;/usr/lib/x86_64-linux-gnu/librt.a -- Build targets : object -- CMake Warning (dev) at /usr/share/cmake-3.31/Modules/FetchContent.cmake:1953 (message): Calling FetchContent_Populate(zlib_ng) is deprecated, call FetchContent_MakeAvailable(zlib_ng) instead. Policy CMP0169 can be set to OLD to allow FetchContent_Populate(zlib_ng) to be called directly for now, but the ability to call it with declared details will be removed completely in a future version. Call Stack (most recent call first): /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/CMakeLists.txt:20 (FetchContent_Populate) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Using CMake version 3.31.6 -- ZLIB_HEADER_VERSION: 1.3.0 -- ZLIBNG_HEADER_VERSION: 2.1.4 -- Arch detected: 'x86_64' -- Basearch of 'x86_64' has been detected as: 'x86' -- Performing Test FNO_LTO_AVAILABLE -- Performing Test FNO_LTO_AVAILABLE - Success -- Looking for arm_acle.h -- Looking for arm_acle.h - not found -- Looking for sys/auxv.h -- Looking for sys/auxv.h - found -- Looking for sys/sdt.h -- Looking for sys/sdt.h - not found -- Looking for unistd.h -- Looking for unistd.h - found -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of off64_t -- Check size of off64_t - done -- Looking for fseeko -- Looking for fseeko - found -- Looking for strerror -- Looking for strerror - found -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for aligned_alloc -- Looking for aligned_alloc - found -- Performing Test HAVE_NO_INTERPOSITION -- Performing Test HAVE_NO_INTERPOSITION - Success -- Performing Test HAVE_ATTRIBUTE_VISIBILITY_HIDDEN -- Performing Test HAVE_ATTRIBUTE_VISIBILITY_HIDDEN - Success -- Performing Test HAVE_ATTRIBUTE_VISIBILITY_INTERNAL -- Performing Test HAVE_ATTRIBUTE_VISIBILITY_INTERNAL - Success -- Performing Test HAVE_ATTRIBUTE_ALIGNED -- Performing Test HAVE_ATTRIBUTE_ALIGNED - Success -- Performing Test HAVE_THREAD_LOCAL -- Performing Test HAVE_THREAD_LOCAL - Success -- Performing Test HAVE_BUILTIN_CTZ -- Performing Test HAVE_BUILTIN_CTZ - Success -- Performing Test HAVE_BUILTIN_CTZLL -- Performing Test HAVE_BUILTIN_CTZLL - Success -- Performing Test HAVE_PTRDIFF_T -- Performing Test HAVE_PTRDIFF_T - Success -- Performing Test HAVE_AVX2_INTRIN -- Performing Test HAVE_AVX2_INTRIN - Success -- Performing Test HAVE_CASCADE_LAKE -- Performing Test HAVE_CASCADE_LAKE - Success -- Performing Test HAVE_AVX512_INTRIN -- Performing Test HAVE_AVX512_INTRIN - Success -- Performing Test HAVE_MASK_INTRIN -- Performing Test HAVE_MASK_INTRIN - Success -- Performing Test HAVE_AVX512VNNI_INTRIN -- Performing Test HAVE_AVX512VNNI_INTRIN - Success -- Performing Test HAVE_SSE42_INTRIN -- Performing Test HAVE_SSE42_INTRIN - Success -- Performing Test HAVE_SSE2_INTRIN -- Performing Test HAVE_SSE2_INTRIN - Success -- Performing Test HAVE_SSSE3_INTRIN -- Performing Test HAVE_SSSE3_INTRIN - Success -- Performing Test HAVE_PCLMULQDQ_INTRIN -- Performing Test HAVE_PCLMULQDQ_INTRIN - Success -- Performing Test HAVE_VPCLMULQDQ_INTRIN -- Performing Test HAVE_VPCLMULQDQ_INTRIN - Success -- Performing Test HAVE_XSAVE_INTRIN -- Performing Test HAVE_XSAVE_INTRIN - Success -- Architecture-specific source files: arch/x86/x86_features.c;arch/x86/slide_hash_avx2.c;arch/x86/chunkset_avx2.c;arch/x86/compare256_avx2.c;arch/x86/adler32_avx2.c;arch/x86/adler32_avx512.c;arch/x86/adler32_avx512_vnni.c;arch/x86/adler32_sse42.c;arch/x86/insert_string_sse42.c;arch/x86/chunkset_sse2.c;arch/x86/compare256_sse2.c;arch/x86/slide_hash_sse2.c;arch/x86/adler32_ssse3.c;arch/x86/chunkset_ssse3.c;arch/x86/crc32_pclmulqdq.c;arch/x86/crc32_vpclmulqdq.c CMake Deprecation Warning at /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/test/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- The following features have been enabled: * CMAKE_BUILD_TYPE, Build type: None (selected) * AVX2_SLIDEHASH, Support AVX2 optimized slide_hash, using "-mavx2" * AVX2_CHUNKSET, Support AVX2 optimized chunkset, using "-mavx2" * AVX2_COMPARE256, Support AVX2 optimized compare256, using "-mavx2" * AVX2_ADLER32, Support AVX2-accelerated adler32, using "-mavx2" * AVX512_ADLER32, Support AVX512-accelerated adler32, using "-mavx512f -mavx512dq -mavx512bw -mavx512vl -mtune=cascadelake" * AVX512VNNI_ADLER32, Support AVX512VNNI adler32, using "-mavx512f -mavx512dq -mavx512bw -mavx512vl -mavx512vnni -mtune=cascadelake" * SSE42_CRC, Support SSE4.2 optimized CRC hash generation, using "-msse4.2" * SSSE3_ADLER32, Support SSSE3-accelerated adler32, using "-mssse3" * PCLMUL_CRC, Support CRC hash generation using PCLMULQDQ, using "-mssse3 -msse4.2 -mpclmul" * VPCLMUL_CRC, Support CRC hash generation using VPCLMULQDQ, using "-mvpclmulqdq -mavx512f -mavx512f -mavx512dq -mavx512bw -mavx512vl -mtune=cascadelake" * XSAVE, Support XSAVE intrinsics using "-mxsave" * WITH_GZFILEOP, Compile with support for gzFile related functions * ZLIB_COMPAT, Compile with zlib compatible API * ZLIB_ENABLE_TESTS, Build test binaries * ZLIBNG_ENABLE_TESTS, Test zlib-ng specific API * WITH_SANITIZER, Enable sanitizer support * WITH_OPTIM, Build with optimisation * WITH_NEW_STRATEGIES, Use new strategies * WITH_AVX2, Build with AVX2 * WITH_AVX512, Build with AVX512 * WITH_AVX512VNNI, Build with AVX512 VNNI * WITH_SSE2, Build with SSE2 * WITH_SSSE3, Build with SSSE3 * WITH_SSE42, Build with SSE42 * WITH_PCLMULQDQ, Build with PCLMULQDQ * WITH_VPCLMULQDQ, Build with VPCLMULQDQ -- The following OPTIONAL packages have been found: * bamtools * OpenMP * Curses -- The following REQUIRED packages have been found: * BZip2 * Boost -- The following features have been disabled: * ZLIB_SYMBOL_PREFIX, Publicly exported symbols DO NOT have a custom prefix * WITH_GTEST, Build gtest_zlib * WITH_FUZZERS, Build test/fuzz * WITH_BENCHMARKS, Build test/benchmarks * WITH_BENCHMARK_APPS, Build application benchmarks * WITH_NATIVE_INSTRUCTIONS, Instruct the compiler to use the full instruction set on this host (gcc/clang -march=native) * WITH_MAINTAINER_WARNINGS, Build with project maintainer warnings * WITH_CODE_COVERAGE, Enable code coverage reporting * WITH_INFLATE_STRICT, Build with strict inflate distance checking * WITH_INFLATE_ALLOW_INVALID_DIST, Build with zero fill for inflate invalid distances * INSTALL_UTILS, Copy minigzip and minideflate during install -- The following OPTIONAL packages have not been found: * Readline -- Looking for open -- Looking for open - found -- Looking for execinfo.h -- Looking for execinfo.h - found -- Looking for signal.h -- Looking for signal.h - found -- Looking for sys/stat.h -- Looking for sys/stat.h - found -- Looking for cxxabi.h -- Looking for cxxabi.h - not found -- Looking for dlfcn.h -- Looking for dlfcn.h - found -- Looking for mach/mach.h -- Looking for mach/mach.h - not found -- Looking for link.h -- Looking for link.h - found -- Looking for sys/mman.h -- Looking for sys/mman.h - found -- Looking for fcntl.h -- Looking for fcntl.h - found -- Looking for malloc/malloc.h -- Looking for malloc/malloc.h - not found -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for sys/time.h -- Looking for sys/time.h - found -- Looking for sys/resource.h -- Looking for sys/resource.h - found -- Looking for backtrace -- Looking for backtrace - found -- backtrace facility detected in default set of libraries -- Found Backtrace: /usr/include -- Looking for futimens -- Looking for futimens - found -- Looking for futimes -- Looking for futimes - found -- Looking for getrusage -- Looking for getrusage - found -- Looking for getpagesize -- Looking for getpagesize - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for mallinfo -- Looking for mallinfo - found -- Looking for mallctl -- Looking for mallctl - not found -- Looking for malloc_zone_statistics -- Looking for malloc_zone_statistics - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Looking for pthread_getspecific in pthread -- Looking for pthread_getspecific in pthread - found -- Looking for pthread_rwlock_init in pthread -- Looking for pthread_rwlock_init in pthread - found -- Looking for pthread_mutex_lock in pthread -- Looking for pthread_mutex_lock in pthread - found -- Looking for dlopen in dl -- Looking for dlopen in dl - found -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Performing Test HAVE_FFI_CALL -- Performing Test HAVE_FFI_CALL - Success -- Found FFI: /usr/lib/x86_64-linux-gnu/libffi.so -- Could NOT find LibEdit (missing: LibEdit_INCLUDE_DIRS LibEdit_LIBRARIES) -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.1") -- Found zstd: /usr/lib/x86_64-linux-gnu/libzstd.so -- Found LibXml2: /usr/lib/x86_64-linux-gnu/libxml2.so (found version "2.9.14") -- Found CURL: /usr/lib/x86_64-linux-gnu/libcurl.so (found version "8.12.1") -- Looking for shm_open -- Looking for shm_open - found CMake Deprecation Warning at /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/CMakeLists.txt:4 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Looking for include file endian.h -- Looking for include file endian.h - found -- Looking for include file inttypes.h -- Looking for include file inttypes.h - found -- Looking for include file strings.h -- Looking for include file strings.h - found -- Looking for include file sys/param.h -- Looking for include file sys/param.h - found -- Looking for include file sys/sysctl.h -- Looking for include file sys/sysctl.h - not found -- Looking for include file netinet/in.h -- Looking for include file netinet/in.h - found -- Performing Test eslENABLE_SSE -- Performing Test eslENABLE_SSE - Success -- Performing Test eslENABLE_SSE4 -- Performing Test eslENABLE_SSE4 - Failed -- Performing Test eslENABLE_AVX -- Performing Test eslENABLE_AVX - Failed -- Performing Test eslENABLE_AVX512 -- Performing Test eslENABLE_AVX512 - Failed -- Performing Test eslENABLE_NEON -- Performing Test eslENABLE_NEON - Failed -- Performing Test eslHAVE_NEON_AARCH64 -- Performing Test eslHAVE_NEON_AARCH64 - Failed -- Performing Test HAVE_FLUSH_ZERO_MODE -- Performing Test HAVE_FLUSH_ZERO_MODE - Success -- Performing Test HAVE_DENORMALS_ZERO_MODE -- Performing Test HAVE_DENORMALS_ZERO_MODE - Failed -- Looking for erfc -- Looking for erfc - not found -- Looking for getpid -- Looking for getpid - found -- Looking for _mm_malloc -- Looking for _mm_malloc - not found -- Looking for popen -- Looking for popen - found -- Looking for strcasecmp -- Looking for strcasecmp - found -- Looking for strsep -- Looking for strsep - found -- Looking for sysctl -- Looking for sysctl - not found -- Looking for times -- Looking for times - found -- Looking for fstat -- Looking for fstat - found -- Looking for getcwd -- Looking for getcwd - found -- Looking for mkstemp -- Looking for mkstemp - found -- Looking for stat -- Looking for stat - found CMake Deprecation Warning at /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/Blaze_Import.cmake:51 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. Call Stack (most recent call first): /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/CMakeLists.txt:7 (Blaze_Import) -- Configuring blaze version 3.8 -- Configured C++11 for multithreading. -- Configuring Vectorization : ON -- Automatic Cache Size Configuration -- Configuring Cache Size : 16777216UL -- Blaze has been configured successfully -- Enabling BayesHammer as a dependency to SPAdes -- Enabling IonHammer as a dependency to SPAdes -- Enabling Corrector as a dependency to SPAdes -- spades project is enabled -- hammer project is enabled -- ionhammer project is enabled -- corrector project is enabled -- spaligner project is disabled -- spades_tools project is enabled -- binspreader project is disabled -- pathracer project is disabled -- mts project is disabled -- online_vis project is disabled -- cds_subgraphs project is disabled -- Configuring done (17.2s) -- Generating done (0.3s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY -- Build files have been written to: /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1' dh_auto_build -- all debruijn_test include_test cd obj-x86_64-linux-gnu && make -j12 "INSTALL=install --strip-program=true" all debruijn_test include_test VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/spades-4.0.0+dfsg1/src -B/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/build.make _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/depend make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/depend make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/depend make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/depend make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/depend make -f ext/lexy/src/CMakeFiles/lexy_file.dir/build.make ext/lexy/src/CMakeFiles/lexy_file.dir/depend make -f ext/easel/CMakeFiles/easel.dir/build.make ext/easel/CMakeFiles/easel.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/cppformat /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/cppformat /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/cppformat/CMakeFiles/format.dir/DependInfo.cmake "--color=" make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/depend make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/gqf /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/gqf /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/gqf/CMakeFiles/gqf.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/edlib /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/edlib /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/edlib/CMakeFiles/edlib.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/DependInfo.cmake "--color=" make -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/lexy/src /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/lexy/src/CMakeFiles/lexy_file.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/teamcity_gtest /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/teamcity_gtest /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/DependInfo.cmake "--color=" make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/depend make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/CMakeFiles/easel.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/coverage_model /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/coverage_model /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/coverage_model/CMakeFiles/coverage_model.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/binary /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/binary/CMakeFiles/binary_io.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/mimalloc /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/mimalloc/CMakeFiles/mimalloc-obj.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils/CMakeFiles/version.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/build make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/build.make _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/build make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/build make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f ext/lexy/src/CMakeFiles/lexy_file.dir/build.make ext/lexy/src/CMakeFiles/lexy_file.dir/build make -f ext/easel/CMakeFiles/easel.dir/build.make ext/easel/CMakeFiles/easel.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 0%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/adler32.c.o [ 0%] Building CXX object ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/build [ 1%] Building CXX object ext/cppformat/CMakeFiles/format.dir/format.cc.o [ 2%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/APFloat.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/adler32.c.o -MF CMakeFiles/zlibstatic.dir/adler32.c.o.d -o CMakeFiles/zlibstatic.dir/adler32.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/adler32.c make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/APFloat.cpp.o -MF CMakeFiles/llvm-support.dir/APFloat.cpp.o.d -o CMakeFiles/llvm-support.dir/APFloat.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/APFloat.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o -MF CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o.d -o CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/teamcity_gtest/teamcity_gtest.cpp make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/build cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/cppformat && /usr/bin/c++ -DFMT_USE_FILE_DESCRIPTORS=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/cppformat -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wall -Wextra -pedantic -Wno-deprecated -O2 -MD -MT ext/cppformat/CMakeFiles/format.dir/format.cc.o -MF CMakeFiles/format.dir/format.cc.o.d -o CMakeFiles/format.dir/format.cc.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/cppformat/format.cc [ 2%] Building C object ext/gqf/CMakeFiles/gqf.dir/gqf.c.o make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 2%] Building CXX object ext/edlib/CMakeFiles/edlib.dir/edlib.cpp.o [ 2%] Building CXX object ext/lexy/src/CMakeFiles/lexy_file.dir/input/file.cpp.o [ 2%] Building C object ext/easel/CMakeFiles/easel.dir/easel.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/gqf && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/gqf/CMakeFiles/gqf.dir/gqf.c.o -MF CMakeFiles/gqf.dir/gqf.c.o.d -o CMakeFiles/gqf.dir/gqf.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/gqf/gqf.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/edlib && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/edlib/CMakeFiles/edlib.dir/edlib.cpp.o -MF CMakeFiles/edlib.dir/edlib.cpp.o.d -o CMakeFiles/edlib.dir/edlib.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/edlib/edlib.cpp [ 2%] Building CXX object common/modules/coverage_model/CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/lexy/src && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -pedantic-errors -Werror -Wall -Wextra -Wconversion -Wsign-conversion -Wno-parentheses -Wno-unused-local-typedefs -Wno-array-bounds -Wno-maybe-uninitialized -Wno-restrict -MD -MT ext/lexy/src/CMakeFiles/lexy_file.dir/input/file.cpp.o -MF CMakeFiles/lexy_file.dir/input/file.cpp.o.d -o CMakeFiles/lexy_file.dir/input/file.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/input/file.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/coverage_model && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/coverage_model/CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o -MF CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o.d -o CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/coverage_model/kmer_coverage_model.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/easel.c.o -MF CMakeFiles/easel.dir/easel.c.o.d -o CMakeFiles/easel.dir/easel.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/easel.c [ 3%] Building CXX object ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/mimalloc && /usr/bin/c++ -DMI_MALLOC_OVERRIDE -DMI_SHOW_ERRORS=1 -DMI_XMALLOC=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -fPIC -Wno-deprecated -O2 -Wall -Wextra -Wno-unknown-pragmas -fvisibility=hidden -ftls-model=initial-exec -fno-builtin-malloc -MD -MT ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o -MF CMakeFiles/mimalloc-obj.dir/src/static.c.o.d -o CMakeFiles/mimalloc-obj.dir/src/static.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/src/static.c [ 4%] Building CXX object common/io/binary/CMakeFiles/binary_io.dir/graph_pack.cpp.o [ 6%] Building CXX object common/utils/CMakeFiles/version.dir/version.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/binary/CMakeFiles/binary_io.dir/graph_pack.cpp.o -MF CMakeFiles/binary_io.dir/graph_pack.cpp.o.d -o CMakeFiles/binary_io.dir/graph_pack.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/utils/CMakeFiles/version.dir/version.cpp.o -MF CMakeFiles/version.dir/version.cpp.o.d -o CMakeFiles/version.dir/version.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/version.cpp /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/gqf/gqf.c: In function 'qf_dump_block': /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/gqf/gqf.c:612:30: warning: format '%llx' expects argument of type 'long long unsigned int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 612 | printf("%02llx ", j); | ~~~~~^ ~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %02lx /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/gqf/gqf.c: In function 'qf_dump': /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/gqf/gqf.c:643:20: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 643 | printf("%llu %llu %llu\n", | ~~~^ | | | long long unsigned int | %lu 644 | qf->metadata->nblocks, | ~~~~~~~~~~~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/gqf/gqf.c:643:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 643 | printf("%llu %llu %llu\n", | ~~~^ | | | long long unsigned int | %lu 644 | qf->metadata->nblocks, 645 | qf->metadata->ndistinct_elts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/gqf/gqf.c:643:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 643 | printf("%llu %llu %llu\n", | ~~~^ | | | long long unsigned int | %lu ...... 646 | qf->metadata->nelts); | ~~~~~~~~~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/gqf/gqf.c: In function 'qf_deserialize': /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/gqf/gqf.c:1609:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1609 | fread(qf->metadata, sizeof(qfmetadata), 1, fin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/gqf/gqf.c:1618:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1618 | fread(qf->blocks, qf->metadata->size, 1, fin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 6%] Linking CXX static library libversion.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -P CMakeFiles/version.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/version.dir/link.txt --verbose=1 [ 6%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/adler32_fold.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/adler32_fold.c.o -MF CMakeFiles/zlibstatic.dir/adler32_fold.c.o.d -o CMakeFiles/zlibstatic.dir/adler32_fold.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/adler32_fold.c /usr/bin/ar qc libversion.a CMakeFiles/version.dir/version.cpp.o /usr/bin/ranlib libversion.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 6%] Built target version make -f common/kmer_index/CMakeFiles/mph_index.dir/build.make common/kmer_index/CMakeFiles/mph_index.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/kmer_index /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/kmer_index/CMakeFiles/mph_index.dir/DependInfo.cmake "--color=" [ 6%] Linking CXX static library liblexy_file.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/lexy/src && /usr/bin/cmake -P CMakeFiles/lexy_file.dir/cmake_clean_target.cmake make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/kmer_index/CMakeFiles/mph_index.dir/build.make common/kmer_index/CMakeFiles/mph_index.dir/build [ 6%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/chunkset.c.o make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/chunkset.c.o -MF CMakeFiles/zlibstatic.dir/chunkset.c.o.d -o CMakeFiles/zlibstatic.dir/chunkset.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/chunkset.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/lexy/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/lexy_file.dir/link.txt --verbose=1 [ 6%] Building CXX object common/kmer_index/CMakeFiles/mph_index.dir/kmer_mph/kmer_buckets.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/kmer_index && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/kmer_index/CMakeFiles/mph_index.dir/kmer_mph/kmer_buckets.cpp.o -MF CMakeFiles/mph_index.dir/kmer_mph/kmer_buckets.cpp.o.d -o CMakeFiles/mph_index.dir/kmer_mph/kmer_buckets.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/kmer_mph/kmer_buckets.cpp /usr/bin/ar qc liblexy_file.a CMakeFiles/lexy_file.dir/input/file.cpp.o /usr/bin/ranlib liblexy_file.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 6%] Built target lexy_file [ 6%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compare256.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compare256.c.o -MF CMakeFiles/zlibstatic.dir/compare256.c.o.d -o CMakeFiles/zlibstatic.dir/compare256.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/compare256.c [ 6%] Building C object ext/easel/CMakeFiles/easel.dir/esl_alloc.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_alloc.c.o -MF CMakeFiles/easel.dir/esl_alloc.c.o.d -o CMakeFiles/easel.dir/esl_alloc.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_alloc.c [ 6%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compress.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compress.c.o -MF CMakeFiles/zlibstatic.dir/compress.c.o.d -o CMakeFiles/zlibstatic.dir/compress.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/compress.c [ 7%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/cpu_features.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/cpu_features.c.o -MF CMakeFiles/zlibstatic.dir/cpu_features.c.o.d -o CMakeFiles/zlibstatic.dir/cpu_features.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/cpu_features.c [ 7%] Building C object ext/easel/CMakeFiles/easel.dir/esl_alphabet.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_alphabet.c.o -MF CMakeFiles/easel.dir/esl_alphabet.c.o.d -o CMakeFiles/easel.dir/esl_alphabet.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_alphabet.c [ 7%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/crc32_braid.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/crc32_braid.c.o -MF CMakeFiles/zlibstatic.dir/crc32_braid.c.o.d -o CMakeFiles/zlibstatic.dir/crc32_braid.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/crc32_braid.c [ 7%] Linking CXX static library libmph_index.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/kmer_index && /usr/bin/cmake -P CMakeFiles/mph_index.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/kmer_index && /usr/bin/cmake -E cmake_link_script CMakeFiles/mph_index.dir/link.txt --verbose=1 /usr/bin/ar qc libmph_index.a CMakeFiles/mph_index.dir/kmer_mph/kmer_buckets.cpp.o /usr/bin/ranlib libmph_index.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 7%] Built target mph_index [ 7%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/crc32_braid_comb.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/crc32_braid_comb.c.o -MF CMakeFiles/zlibstatic.dir/crc32_braid_comb.c.o.d -o CMakeFiles/zlibstatic.dir/crc32_braid_comb.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/crc32_braid_comb.c [ 7%] Building C object ext/easel/CMakeFiles/easel.dir/esl_arr2.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_arr2.c.o -MF CMakeFiles/easel.dir/esl_arr2.c.o.d -o CMakeFiles/easel.dir/esl_arr2.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_arr2.c [ 7%] Linking C static library libgqf.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/gqf && /usr/bin/cmake -P CMakeFiles/gqf.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/gqf && /usr/bin/cmake -E cmake_link_script CMakeFiles/gqf.dir/link.txt --verbose=1 [ 7%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/crc32_fold.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/crc32_fold.c.o -MF CMakeFiles/zlibstatic.dir/crc32_fold.c.o.d -o CMakeFiles/zlibstatic.dir/crc32_fold.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/crc32_fold.c /usr/bin/ar qc libgqf.a CMakeFiles/gqf.dir/gqf.c.o /usr/bin/ranlib libgqf.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 7%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate.c.o -MF CMakeFiles/zlibstatic.dir/deflate.c.o.d -o CMakeFiles/zlibstatic.dir/deflate.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/deflate.c [ 7%] Built target gqf [ 7%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_fast.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_fast.c.o -MF CMakeFiles/zlibstatic.dir/deflate_fast.c.o.d -o CMakeFiles/zlibstatic.dir/deflate_fast.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/deflate_fast.c [ 7%] Building C object ext/easel/CMakeFiles/easel.dir/esl_arr3.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_arr3.c.o -MF CMakeFiles/easel.dir/esl_arr3.c.o.d -o CMakeFiles/easel.dir/esl_arr3.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_arr3.c [ 8%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_huff.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_huff.c.o -MF CMakeFiles/zlibstatic.dir/deflate_huff.c.o.d -o CMakeFiles/zlibstatic.dir/deflate_huff.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/deflate_huff.c [ 8%] Building C object ext/easel/CMakeFiles/easel.dir/esl_buffer.c.o [ 9%] Building C object ext/easel/CMakeFiles/easel.dir/esl_bitfield.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_buffer.c.o -MF CMakeFiles/easel.dir/esl_buffer.c.o.d -o CMakeFiles/easel.dir/esl_buffer.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_buffer.c [ 9%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_medium.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_bitfield.c.o -MF CMakeFiles/easel.dir/esl_bitfield.c.o.d -o CMakeFiles/easel.dir/esl_bitfield.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_bitfield.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_medium.c.o -MF CMakeFiles/zlibstatic.dir/deflate_medium.c.o.d -o CMakeFiles/zlibstatic.dir/deflate_medium.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/deflate_medium.c [ 9%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_quick.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_quick.c.o -MF CMakeFiles/zlibstatic.dir/deflate_quick.c.o.d -o CMakeFiles/zlibstatic.dir/deflate_quick.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/deflate_quick.c [ 9%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_rle.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_rle.c.o -MF CMakeFiles/zlibstatic.dir/deflate_rle.c.o.d -o CMakeFiles/zlibstatic.dir/deflate_rle.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/deflate_rle.c [ 9%] Building CXX object ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o -MF CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o.d -o CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/teamcity_gtest/teamcity_messages.cpp [ 9%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_slow.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_slow.c.o -MF CMakeFiles/zlibstatic.dir/deflate_slow.c.o.d -o CMakeFiles/zlibstatic.dir/deflate_slow.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/deflate_slow.c [ 9%] Building C object ext/easel/CMakeFiles/easel.dir/esl_cluster.c.o [ 9%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_stored.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_cluster.c.o -MF CMakeFiles/easel.dir/esl_cluster.c.o.d -o CMakeFiles/easel.dir/esl_cluster.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_cluster.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_stored.c.o -MF CMakeFiles/zlibstatic.dir/deflate_stored.c.o.d -o CMakeFiles/zlibstatic.dir/deflate_stored.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/deflate_stored.c [ 10%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/functable.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/functable.c.o -MF CMakeFiles/zlibstatic.dir/functable.c.o.d -o CMakeFiles/zlibstatic.dir/functable.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/functable.c [ 10%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/infback.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/infback.c.o -MF CMakeFiles/zlibstatic.dir/infback.c.o.d -o CMakeFiles/zlibstatic.dir/infback.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/infback.c [ 10%] Building C object ext/easel/CMakeFiles/easel.dir/esl_composition.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_composition.c.o -MF CMakeFiles/easel.dir/esl_composition.c.o.d -o CMakeFiles/easel.dir/esl_composition.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_composition.c [ 10%] Building C object ext/easel/CMakeFiles/easel.dir/esl_cpu.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_cpu.c.o -MF CMakeFiles/easel.dir/esl_cpu.c.o.d -o CMakeFiles/easel.dir/esl_cpu.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_cpu.c [ 10%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/inflate.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/inflate.c.o -MF CMakeFiles/zlibstatic.dir/inflate.c.o.d -o CMakeFiles/zlibstatic.dir/inflate.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/inflate.c [ 12%] Building C object ext/easel/CMakeFiles/easel.dir/esl_distance.c.o [ 12%] Building C object ext/easel/CMakeFiles/easel.dir/esl_dirichlet.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_distance.c.o -MF CMakeFiles/easel.dir/esl_distance.c.o.d -o CMakeFiles/easel.dir/esl_distance.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_distance.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_dirichlet.c.o -MF CMakeFiles/easel.dir/esl_dirichlet.c.o.d -o CMakeFiles/easel.dir/esl_dirichlet.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_dirichlet.c [ 12%] Linking CXX static library libedlib.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/edlib && /usr/bin/cmake -P CMakeFiles/edlib.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/edlib && /usr/bin/cmake -E cmake_link_script CMakeFiles/edlib.dir/link.txt --verbose=1 [ 12%] Building C object ext/easel/CMakeFiles/easel.dir/esl_dmatrix.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_dmatrix.c.o -MF CMakeFiles/easel.dir/esl_dmatrix.c.o.d -o CMakeFiles/easel.dir/esl_dmatrix.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_dmatrix.c [ 12%] Building C object ext/easel/CMakeFiles/easel.dir/esl_dsqdata.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_dsqdata.c.o -MF CMakeFiles/easel.dir/esl_dsqdata.c.o.d -o CMakeFiles/easel.dir/esl_dsqdata.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_dsqdata.c [ 12%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/inftrees.c.o /usr/bin/ar qc libedlib.a CMakeFiles/edlib.dir/edlib.cpp.o /usr/bin/ranlib libedlib.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/inftrees.c.o -MF CMakeFiles/zlibstatic.dir/inftrees.c.o.d -o CMakeFiles/zlibstatic.dir/inftrees.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/inftrees.c make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 12%] Built target edlib make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/sequence /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/sequence/CMakeFiles/sequence.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 12%] Building CXX object common/sequence/CMakeFiles/sequence.dir/sequence_tools.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/sequence && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/sequence/CMakeFiles/sequence.dir/sequence_tools.cpp.o -MF CMakeFiles/sequence.dir/sequence_tools.cpp.o.d -o CMakeFiles/sequence.dir/sequence_tools.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/sequence_tools.cpp [ 12%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/insert_string.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/insert_string.c.o -MF CMakeFiles/zlibstatic.dir/insert_string.c.o.d -o CMakeFiles/zlibstatic.dir/insert_string.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/insert_string.c [ 13%] Linking CXX static library libteamcity_gtest.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/cmake -P CMakeFiles/teamcity_gtest.dir/cmake_clean_target.cmake [ 13%] Building C object ext/easel/CMakeFiles/easel.dir/esl_exponential.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_exponential.c.o -MF CMakeFiles/easel.dir/esl_exponential.c.o.d -o CMakeFiles/easel.dir/esl_exponential.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_exponential.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/teamcity_gtest.dir/link.txt --verbose=1 [ 13%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/insert_string_roll.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/insert_string_roll.c.o -MF CMakeFiles/zlibstatic.dir/insert_string_roll.c.o.d -o CMakeFiles/zlibstatic.dir/insert_string_roll.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/insert_string_roll.c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/coverage_model/kmer_coverage_model.cpp: In member function 'void coverage_model::KMerCoverageModel::Fit()': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/coverage_model/kmer_coverage_model.cpp:326:23: warning: conversion from 'size_t' {aka 'long unsigned int'} to '__gnu_cxx::__alloc_traits, double>::value_type' {aka 'double'} may change value [-Wconversion] 326 | if (converged_ && Valley_ > x[2] && x[2] > 2) { | ^~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/coverage_model/kmer_coverage_model.cpp:360:28: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 360 | ErrorThreshold_ = (Valley_ < mean_coverage_ ? | ^~~~~~~ /usr/bin/ar qc libteamcity_gtest.a CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o /usr/bin/ranlib libteamcity_gtest.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 13%] Building C object ext/easel/CMakeFiles/easel.dir/esl_fileparser.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_fileparser.c.o -MF CMakeFiles/easel.dir/esl_fileparser.c.o.d -o CMakeFiles/easel.dir/esl_fileparser.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_fileparser.c [ 13%] Built target teamcity_gtest [ 14%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/slide_hash.c.o [ 14%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/trees.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/slide_hash.c.o -MF CMakeFiles/zlibstatic.dir/slide_hash.c.o.d -o CMakeFiles/zlibstatic.dir/slide_hash.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/slide_hash.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/trees.c.o -MF CMakeFiles/zlibstatic.dir/trees.c.o.d -o CMakeFiles/zlibstatic.dir/trees.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/trees.c [ 14%] Building CXX object common/io/binary/CMakeFiles/binary_io.dir/genomic_info.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/binary/CMakeFiles/binary_io.dir/genomic_info.cpp.o -MF CMakeFiles/binary_io.dir/genomic_info.cpp.o.d -o CMakeFiles/binary_io.dir/genomic_info.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/genomic_info.cpp /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp: In member function 'virtual bool io::binary::FullPackIO::BinRead(std::istream&, Type&)': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:364:10: warning: unused variable 'loaded' [-Wunused-variable] 364 | bool loaded = base::BinRead(is, gp); | ^~~~~~ [ 14%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gamma.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_gamma.c.o -MF CMakeFiles/easel.dir/esl_gamma.c.o.d -o CMakeFiles/easel.dir/esl_gamma.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_gamma.c [ 14%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/uncompr.c.o [ 14%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/zutil.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/uncompr.c.o -MF CMakeFiles/zlibstatic.dir/uncompr.c.o.d -o CMakeFiles/zlibstatic.dir/uncompr.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/uncompr.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/zutil.c.o -MF CMakeFiles/zlibstatic.dir/zutil.c.o.d -o CMakeFiles/zlibstatic.dir/zutil.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/zutil.c [ 15%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gencode.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_gencode.c.o -MF CMakeFiles/easel.dir/esl_gencode.c.o.d -o CMakeFiles/easel.dir/esl_gencode.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_gencode.c In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:8: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:208:19: required from here 208 | graph_io_.Load(basename, g); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:31:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 31 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::Loader::Load() [with T = omnigraph::EdgesPositionHandler]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:211:45: required from here 211 | loader.Load>(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:102:14: warning: unused variable 'loaded' [-Wunused-variable] 102 | bool loaded = io.Load(basename, component); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::Loader::Load() [with T = debruijn_graph::EdgeIndex]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:214:34: required from here 214 | loader.Load>(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:102:14: warning: unused variable 'loaded' [-Wunused-variable] 102 | bool loaded = io.Load(basename, component); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::Loader::Load() [with T = debruijn_graph::KmerMapper]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:217:35: required from here 217 | loader.Load>(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:102:14: warning: unused variable 'loaded' [-Wunused-variable] 102 | bool loaded = io.Load(basename, component); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::Loader::Load() [with T = omnigraph::FlankingCoverage]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:220:41: required from here 220 | loader.Load>(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:102:14: warning: unused variable 'loaded' [-Wunused-variable] 102 | bool loaded = io.Load(basename, component); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:254:22: required from here 254 | graph_io_.BinRead(is, gp.get_mutable()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:44:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 44 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::BinReader::Read() [with T = omnigraph::EdgesPositionHandler]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:257:45: required from here 257 | reader.Read>(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:131:14: warning: unused variable 'loaded' [-Wunused-variable] 131 | auto loaded = io.BinRead(is, component); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::BinReader::Read() [with T = debruijn_graph::EdgeIndex]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:260:34: required from here 260 | reader.Read>(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:131:14: warning: unused variable 'loaded' [-Wunused-variable] 131 | auto loaded = io.BinRead(is, component); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::BinReader::Read() [with T = debruijn_graph::KmerMapper]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:263:35: required from here 263 | reader.Read>(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:131:14: warning: unused variable 'loaded' [-Wunused-variable] 131 | auto loaded = io.BinRead(is, component); | ^~~~~~ [ 15%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/x86_features.c.o /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::BinReader::Read() [with T = omnigraph::FlankingCoverage]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:266:41: required from here 266 | reader.Read>(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:131:14: warning: unused variable 'loaded' [-Wunused-variable] 131 | auto loaded = io.BinRead(is, component); | ^~~~~~ cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -mxsave -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/x86_features.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/x86_features.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/x86_features.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/x86_features.c [ 15%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/slide_hash_avx2.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -mavx2 -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/slide_hash_avx2.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/slide_hash_avx2.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/slide_hash_avx2.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/slide_hash_avx2.c [ 17%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/chunkset_avx2.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -mavx2 -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/chunkset_avx2.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/chunkset_avx2.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/chunkset_avx2.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/chunkset_avx2.c [ 17%] Building C object ext/easel/CMakeFiles/easel.dir/esl_getopts.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_getopts.c.o -MF CMakeFiles/easel.dir/esl_getopts.c.o.d -o CMakeFiles/easel.dir/esl_getopts.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_getopts.c [ 17%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/compare256_avx2.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -mavx2 -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/compare256_avx2.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/compare256_avx2.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/compare256_avx2.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/compare256_avx2.c [ 17%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx2.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -mavx2 -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx2.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx2.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx2.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/adler32_avx2.c [ 17%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx512.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -mavx512f -mavx512dq -mavx512bw -mavx512vl -mtune=cascadelake -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx512.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx512.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx512.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/adler32_avx512.c In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:10: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:47:10: required from here 47 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:61:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 61 | auto new_id = graph.AddVertex(typename Graph::VertexData(graph.k()), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:83:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 83 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ [ 17%] Building CXX object ext/cppformat/CMakeFiles/format.dir/posix.cc.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/cppformat && /usr/bin/c++ -DFMT_USE_FILE_DESCRIPTORS=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/cppformat -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wall -Wextra -pedantic -Wno-deprecated -O2 -MD -MT ext/cppformat/CMakeFiles/format.dir/posix.cc.o -MF CMakeFiles/format.dir/posix.cc.o.d -o CMakeFiles/format.dir/posix.cc.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/cppformat/posix.cc [ 17%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx512_vnni.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -mavx512f -mavx512dq -mavx512bw -mavx512vl -mavx512vnni -mtune=cascadelake -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx512_vnni.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx512_vnni.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx512_vnni.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/adler32_avx512_vnni.c [ 17%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gev.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_gev.c.o -MF CMakeFiles/easel.dir/esl_gev.c.o.d -o CMakeFiles/easel.dir/esl_gev.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_gev.c [ 17%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_sse42.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -msse4.2 -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_sse42.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/adler32_sse42.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/adler32_sse42.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/adler32_sse42.c [ 18%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/insert_string_sse42.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -msse4.2 -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/insert_string_sse42.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/insert_string_sse42.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/insert_string_sse42.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/insert_string_sse42.c [ 18%] Linking CXX static library libsequence.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/sequence && /usr/bin/cmake -P CMakeFiles/sequence.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/sequence && /usr/bin/cmake -E cmake_link_script CMakeFiles/sequence.dir/link.txt --verbose=1 [ 18%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/chunkset_sse2.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/chunkset_sse2.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/chunkset_sse2.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/chunkset_sse2.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/chunkset_sse2.c [ 18%] Building C object ext/easel/CMakeFiles/easel.dir/esl_graph.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_graph.c.o -MF CMakeFiles/easel.dir/esl_graph.c.o.d -o CMakeFiles/easel.dir/esl_graph.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_graph.c [ 18%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gumbel.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_gumbel.c.o -MF CMakeFiles/easel.dir/esl_gumbel.c.o.d -o CMakeFiles/easel.dir/esl_gumbel.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_gumbel.c /usr/bin/ar qc libsequence.a CMakeFiles/sequence.dir/sequence_tools.cpp.o /usr/bin/ranlib libsequence.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 18%] Built target sequence [ 18%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/compare256_sse2.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/compare256_sse2.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/compare256_sse2.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/compare256_sse2.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/compare256_sse2.c [ 18%] Building C object ext/easel/CMakeFiles/easel.dir/esl_heap.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_heap.c.o -MF CMakeFiles/easel.dir/esl_heap.c.o.d -o CMakeFiles/easel.dir/esl_heap.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_heap.c [ 18%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/slide_hash_sse2.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/slide_hash_sse2.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/slide_hash_sse2.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/slide_hash_sse2.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/slide_hash_sse2.c [ 19%] Building C object ext/easel/CMakeFiles/easel.dir/esl_histogram.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_histogram.c.o -MF CMakeFiles/easel.dir/esl_histogram.c.o.d -o CMakeFiles/easel.dir/esl_histogram.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_histogram.c [ 19%] Building C object ext/easel/CMakeFiles/easel.dir/esl_hmm.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_hmm.c.o -MF CMakeFiles/easel.dir/esl_hmm.c.o.d -o CMakeFiles/easel.dir/esl_hmm.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_hmm.c [ 19%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_ssse3.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -mssse3 -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_ssse3.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/adler32_ssse3.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/adler32_ssse3.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/adler32_ssse3.c [ 19%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/chunkset_ssse3.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -mssse3 -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/chunkset_ssse3.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/chunkset_ssse3.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/chunkset_ssse3.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/chunkset_ssse3.c [ 19%] Linking CXX static library libformat.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/cppformat && /usr/bin/cmake -P CMakeFiles/format.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/cppformat && /usr/bin/cmake -E cmake_link_script CMakeFiles/format.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 19%] Built target mimalloc-obj [ 20%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/crc32_pclmulqdq.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -mssse3 -msse4.2 -mpclmul -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/crc32_pclmulqdq.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/crc32_pclmulqdq.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/crc32_pclmulqdq.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/crc32_pclmulqdq.c /usr/bin/ar qc libformat.a CMakeFiles/format.dir/format.cc.o CMakeFiles/format.dir/posix.cc.o /usr/bin/ranlib libformat.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 20%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/crc32_vpclmulqdq.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -mssse3 -msse4.2 -mpclmul -mvpclmulqdq -mavx512f -mavx512f -mavx512dq -mavx512bw -mavx512vl -mtune=cascadelake -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/crc32_vpclmulqdq.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/crc32_vpclmulqdq.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/crc32_vpclmulqdq.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/crc32_vpclmulqdq.c [ 20%] Built target format make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 20%] Building C object ext/easel/CMakeFiles/easel.dir/esl_huffman.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_huffman.c.o -MF CMakeFiles/easel.dir/esl_huffman.c.o.d -o CMakeFiles/easel.dir/esl_huffman.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_huffman.c [ 20%] Building CXX object common/utils/CMakeFiles/utils.dir/memory_limit.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/utils/CMakeFiles/utils.dir/memory_limit.cpp.o -MF CMakeFiles/utils.dir/memory_limit.cpp.o.d -o CMakeFiles/utils.dir/memory_limit.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/memory_limit.cpp [ 20%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/path_helper.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/utils/CMakeFiles/utils.dir/filesystem/path_helper.cpp.o -MF CMakeFiles/utils.dir/filesystem/path_helper.cpp.o.d -o CMakeFiles/utils.dir/filesystem/path_helper.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/filesystem/path_helper.cpp [ 20%] Building C object ext/easel/CMakeFiles/easel.dir/esl_hyperexp.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_hyperexp.c.o -MF CMakeFiles/easel.dir/esl_hyperexp.c.o.d -o CMakeFiles/easel.dir/esl_hyperexp.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_hyperexp.c [ 20%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/gzlib.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/gzlib.c.o -MF CMakeFiles/zlibstatic.dir/gzlib.c.o.d -o CMakeFiles/zlibstatic.dir/gzlib.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/gzlib.c [ 20%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/gzread.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/gzread.c.o -MF CMakeFiles/zlibstatic.dir/gzread.c.o.d -o CMakeFiles/zlibstatic.dir/gzread.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/gzread.c [ 20%] Building C object ext/easel/CMakeFiles/easel.dir/esl_iset.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_iset.c.o -MF CMakeFiles/easel.dir/esl_iset.c.o.d -o CMakeFiles/easel.dir/esl_iset.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_iset.c [ 20%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/gzwrite.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/gzwrite.c.o -MF CMakeFiles/zlibstatic.dir/gzwrite.c.o.d -o CMakeFiles/zlibstatic.dir/gzwrite.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/gzwrite.c [ 20%] Building C object ext/easel/CMakeFiles/easel.dir/esl_json.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_json.c.o -MF CMakeFiles/easel.dir/esl_json.c.o.d -o CMakeFiles/easel.dir/esl_json.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_json.c [ 20%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/temporary.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ 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/build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/filesystem/temporary.cpp [ 21%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/glob.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/utils/CMakeFiles/utils.dir/filesystem/glob.cpp.o -MF CMakeFiles/utils.dir/filesystem/glob.cpp.o.d -o CMakeFiles/utils.dir/filesystem/glob.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/filesystem/glob.cpp [ 23%] Building C object ext/easel/CMakeFiles/easel.dir/esl_keyhash.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_keyhash.c.o -MF CMakeFiles/easel.dir/esl_keyhash.c.o.d -o CMakeFiles/easel.dir/esl_keyhash.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_keyhash.c [ 23%] Building C object ext/easel/CMakeFiles/easel.dir/esl_lognormal.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_lognormal.c.o -MF CMakeFiles/easel.dir/esl_lognormal.c.o.d -o CMakeFiles/easel.dir/esl_lognormal.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_lognormal.c [ 24%] Linking C static library libz.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cmake -P CMakeFiles/zlibstatic.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cmake -E cmake_link_script CMakeFiles/zlibstatic.dir/link.txt --verbose=1 [ 24%] Building C object ext/easel/CMakeFiles/easel.dir/esl_mem.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_mem.c.o -MF CMakeFiles/easel.dir/esl_mem.c.o.d -o CMakeFiles/easel.dir/esl_mem.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_mem.c [ 24%] Building C object ext/easel/CMakeFiles/easel.dir/esl_matrixops.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_matrixops.c.o -MF CMakeFiles/easel.dir/esl_matrixops.c.o.d -o CMakeFiles/easel.dir/esl_matrixops.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_matrixops.c [ 24%] Building C object ext/easel/CMakeFiles/easel.dir/esl_minimizer.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_minimizer.c.o -MF CMakeFiles/easel.dir/esl_minimizer.c.o.d -o CMakeFiles/easel.dir/esl_minimizer.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_minimizer.c [ 24%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/APInt.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/APInt.cpp.o -MF CMakeFiles/llvm-support.dir/APInt.cpp.o.d -o CMakeFiles/llvm-support.dir/APInt.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/APInt.cpp /usr/bin/ar qc libz.a CMakeFiles/zlibstatic.dir/adler32.c.o CMakeFiles/zlibstatic.dir/adler32_fold.c.o CMakeFiles/zlibstatic.dir/chunkset.c.o CMakeFiles/zlibstatic.dir/compare256.c.o CMakeFiles/zlibstatic.dir/compress.c.o CMakeFiles/zlibstatic.dir/cpu_features.c.o CMakeFiles/zlibstatic.dir/crc32_braid.c.o CMakeFiles/zlibstatic.dir/crc32_braid_comb.c.o CMakeFiles/zlibstatic.dir/crc32_fold.c.o CMakeFiles/zlibstatic.dir/deflate.c.o CMakeFiles/zlibstatic.dir/deflate_fast.c.o CMakeFiles/zlibstatic.dir/deflate_huff.c.o CMakeFiles/zlibstatic.dir/deflate_medium.c.o CMakeFiles/zlibstatic.dir/deflate_quick.c.o CMakeFiles/zlibstatic.dir/deflate_rle.c.o CMakeFiles/zlibstatic.dir/deflate_slow.c.o CMakeFiles/zlibstatic.dir/deflate_stored.c.o CMakeFiles/zlibstatic.dir/functable.c.o CMakeFiles/zlibstatic.dir/infback.c.o CMakeFiles/zlibstatic.dir/inflate.c.o CMakeFiles/zlibstatic.dir/inftrees.c.o CMakeFiles/zlibstatic.dir/insert_string.c.o CMakeFiles/zlibstatic.dir/insert_string_roll.c.o CMakeFiles/zlibstatic.dir/slide_hash.c.o CMakeFiles/zlibstatic.dir/trees.c.o CMakeFiles/zlibstatic.dir/uncompr.c.o CMakeFiles/zlibstatic.dir/zutil.c.o CMakeFiles/zlibstatic.dir/arch/x86/x86_features.c.o CMakeFiles/zlibstatic.dir/arch/x86/slide_hash_avx2.c.o CMakeFiles/zlibstatic.dir/arch/x86/chunkset_avx2.c.o CMakeFiles/zlibstatic.dir/arch/x86/compare256_avx2.c.o CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx2.c.o CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx512.c.o CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx512_vnni.c.o CMakeFiles/zlibstatic.dir/arch/x86/adler32_sse42.c.o CMakeFiles/zlibstatic.dir/arch/x86/insert_string_sse42.c.o CMakeFiles/zlibstatic.dir/arch/x86/chunkset_sse2.c.o CMakeFiles/zlibstatic.dir/arch/x86/compare256_sse2.c.o CMakeFiles/zlibstatic.dir/arch/x86/slide_hash_sse2.c.o CMakeFiles/zlibstatic.dir/arch/x86/adler32_ssse3.c.o CMakeFiles/zlibstatic.dir/arch/x86/chunkset_ssse3.c.o CMakeFiles/zlibstatic.dir/arch/x86/crc32_pclmulqdq.c.o CMakeFiles/zlibstatic.dir/arch/x86/crc32_vpclmulqdq.c.o CMakeFiles/zlibstatic.dir/gzlib.c.o CMakeFiles/zlibstatic.dir/gzread.c.o CMakeFiles/zlibstatic.dir/gzwrite.c.o /usr/bin/ranlib libz.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 24%] Built target zlibstatic make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/build make[4]: 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-I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_aux.c.o -MF CMakeFiles/samtools.dir/bam_aux.c.o.d -o CMakeFiles/samtools.dir/bam_aux.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_aux.c [ 25%] Building C object ext/easel/CMakeFiles/easel.dir/esl_mixdchlet.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_mixdchlet.c.o -MF CMakeFiles/easel.dir/esl_mixdchlet.c.o.d -o CMakeFiles/easel.dir/esl_mixdchlet.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_mixdchlet.c [ 26%] Building C object ext/easel/CMakeFiles/easel.dir/esl_mixgev.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_mixgev.c.o -MF CMakeFiles/easel.dir/esl_mixgev.c.o.d -o CMakeFiles/easel.dir/esl_mixgev.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_mixgev.c [ 26%] Building C object ext/easel/CMakeFiles/easel.dir/esl_mpi.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_mpi.c.o -MF CMakeFiles/easel.dir/esl_mpi.c.o.d -o CMakeFiles/easel.dir/esl_mpi.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_mpi.c [ 26%] Linking CXX static library libcoverage_model.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/coverage_model && /usr/bin/cmake -P CMakeFiles/coverage_model.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/coverage_model && /usr/bin/cmake -E cmake_link_script CMakeFiles/coverage_model.dir/link.txt --verbose=1 [ 26%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msa.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msa.c.o -MF CMakeFiles/easel.dir/esl_msa.c.o.d -o CMakeFiles/easel.dir/esl_msa.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_msa.c [ 26%] Building CXX object common/utils/CMakeFiles/utils.dir/logger/logger_impl.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG 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/build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/logger/logger_impl.cpp [ 26%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msacluster.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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ext/bwa/CMakeFiles/bwa.dir/utils.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile2.c.o -MF CMakeFiles/easel.dir/esl_msafile2.c.o.d -o CMakeFiles/easel.dir/esl_msafile2.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_msafile2.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/utils.c.o -MF CMakeFiles/bwa.dir/utils.c.o.d -o CMakeFiles/bwa.dir/utils.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/utils.c [ 28%] Building CXX object common/utils/CMakeFiles/utils.dir/logger/log_writers.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/utils/CMakeFiles/utils.dir/logger/log_writers.cpp.o -MF CMakeFiles/utils.dir/logger/log_writers.cpp.o.d -o CMakeFiles/utils.dir/logger/log_writers.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/logger/log_writers.cpp [ 28%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_import.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_import.c.o -MF CMakeFiles/samtools.dir/bam_import.c.o.d -o CMakeFiles/samtools.dir/bam_import.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_import.c [ 28%] Building CXX object common/utils/CMakeFiles/utils.dir/logger/log_writers_thread.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/utils/CMakeFiles/utils.dir/logger/log_writers_thread.cpp.o -MF CMakeFiles/utils.dir/logger/log_writers_thread.cpp.o.d -o CMakeFiles/utils.dir/logger/log_writers_thread.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/logger/log_writers_thread.cpp [ 28%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_a2m.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_a2m.c.o -MF CMakeFiles/easel.dir/esl_msafile_a2m.c.o.d -o CMakeFiles/easel.dir/esl_msafile_a2m.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_msafile_a2m.c [ 28%] Building C object ext/bwa/CMakeFiles/bwa.dir/kthread.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/kthread.c.o -MF CMakeFiles/bwa.dir/kthread.c.o.d -o CMakeFiles/bwa.dir/kthread.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/kthread.c [ 28%] Building C object ext/bwa/CMakeFiles/bwa.dir/ksw.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/ksw.c.o -MF CMakeFiles/bwa.dir/ksw.c.o.d -o CMakeFiles/bwa.dir/ksw.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/ksw.c [ 28%] Building C object ext/samtools/CMakeFiles/samtools.dir/sam.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/sam.c.o -MF CMakeFiles/samtools.dir/sam.c.o.d -o CMakeFiles/samtools.dir/sam.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/sam.c [ 29%] Building C object ext/bwa/CMakeFiles/bwa.dir/bwt.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/bwt.c.o -MF CMakeFiles/bwa.dir/bwt.c.o.d -o CMakeFiles/bwa.dir/bwt.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwt.c [ 29%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_afa.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_afa.c.o -MF CMakeFiles/easel.dir/esl_msafile_afa.c.o.d -o CMakeFiles/easel.dir/esl_msafile_afa.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_msafile_afa.c [ 29%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_clustal.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_clustal.c.o -MF CMakeFiles/easel.dir/esl_msafile_clustal.c.o.d -o CMakeFiles/easel.dir/esl_msafile_clustal.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_msafile_clustal.c [ 29%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_index.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_index.c.o -MF CMakeFiles/samtools.dir/bam_index.c.o.d -o CMakeFiles/samtools.dir/bam_index.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_index.c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_index.c: In function 'bam_index_load_core': /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_index.c:335:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 335 | fread(magic, 1, 4, fp); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_index.c:342:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 342 | fread(&idx->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_index.c:355:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 355 | fread(&size, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_index.c:358:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 358 | fread(&key, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_index.c:362:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 362 | fread(&p->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_index.c:366:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 366 | fread(p->list, 16, p->n, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_index.c:376:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 376 | fread(&index2->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_index.c:380:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 380 | fread(index2->offset, index2->n, 8, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 29%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_phylip.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_phylip.c.o -MF CMakeFiles/easel.dir/esl_msafile_phylip.c.o.d -o CMakeFiles/easel.dir/esl_msafile_phylip.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_msafile_phylip.c [ 29%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_psiblast.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_psiblast.c.o -MF CMakeFiles/easel.dir/esl_msafile_psiblast.c.o.d -o CMakeFiles/easel.dir/esl_msafile_psiblast.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_msafile_psiblast.c [ 29%] Building C object ext/bwa/CMakeFiles/bwa.dir/bntseq.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/bntseq.c.o -MF CMakeFiles/bwa.dir/bntseq.c.o.d -o CMakeFiles/bwa.dir/bntseq.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bntseq.c [ 29%] Building C object ext/bwa/CMakeFiles/bwa.dir/bwa.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/bwa.c.o -MF CMakeFiles/bwa.dir/bwa.c.o.d -o CMakeFiles/bwa.dir/bwa.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwa.c [ 30%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_selex.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_selex.c.o -MF CMakeFiles/easel.dir/esl_msafile_selex.c.o.d -o CMakeFiles/easel.dir/esl_msafile_selex.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_msafile_selex.c [ 30%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_stockholm.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_stockholm.c.o -MF CMakeFiles/easel.dir/esl_msafile_stockholm.c.o.d -o CMakeFiles/easel.dir/esl_msafile_stockholm.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_msafile_stockholm.c [ 30%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msashuffle.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msashuffle.c.o -MF CMakeFiles/easel.dir/esl_msashuffle.c.o.d -o CMakeFiles/easel.dir/esl_msashuffle.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_msashuffle.c [ 30%] Building C object ext/bwa/CMakeFiles/bwa.dir/bwamem.c.o [ 30%] Building C object ext/bwa/CMakeFiles/bwa.dir/bwamem_pair.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/bwamem.c.o -MF CMakeFiles/bwa.dir/bwamem.c.o.d -o CMakeFiles/bwa.dir/bwamem.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwamem.c [ 30%] Building C object ext/bwa/CMakeFiles/bwa.dir/bwamem_extra.c.o [ 30%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msaweight.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/bwamem_pair.c.o -MF CMakeFiles/bwa.dir/bwamem_pair.c.o.d -o CMakeFiles/bwa.dir/bwamem_pair.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwamem_pair.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msaweight.c.o -MF CMakeFiles/easel.dir/esl_msaweight.c.o.d -o CMakeFiles/easel.dir/esl_msaweight.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_msaweight.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/bwamem_extra.c.o -MF CMakeFiles/bwa.dir/bwamem_extra.c.o.d -o CMakeFiles/bwa.dir/bwamem_extra.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwamem_extra.c [ 31%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_pileup.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_pileup.c.o -MF CMakeFiles/samtools.dir/bam_pileup.c.o.d -o CMakeFiles/samtools.dir/bam_pileup.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_pileup.c [ 32%] Building C object ext/bwa/CMakeFiles/bwa.dir/malloc_wrap.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/malloc_wrap.c.o -MF CMakeFiles/bwa.dir/malloc_wrap.c.o.d -o CMakeFiles/bwa.dir/malloc_wrap.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/malloc_wrap.c [ 32%] Building C object ext/easel/CMakeFiles/easel.dir/esl_normal.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_normal.c.o -MF CMakeFiles/easel.dir/esl_normal.c.o.d -o CMakeFiles/easel.dir/esl_normal.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_normal.c [ 32%] Building C object ext/bwa/CMakeFiles/bwa.dir/is.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/is.c.o -MF CMakeFiles/bwa.dir/is.c.o.d -o CMakeFiles/bwa.dir/is.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/is.c [ 32%] Building C object ext/easel/CMakeFiles/easel.dir/esl_paml.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_paml.c.o -MF CMakeFiles/easel.dir/esl_paml.c.o.d -o CMakeFiles/easel.dir/esl_paml.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_paml.c [ 32%] Linking CXX static library libutils.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake [ 32%] Building C object ext/bwa/CMakeFiles/bwa.dir/bwtindex.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/bwtindex.c.o -MF CMakeFiles/bwa.dir/bwtindex.c.o.d -o CMakeFiles/bwa.dir/bwtindex.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwtindex.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 [ 34%] Building C object ext/easel/CMakeFiles/easel.dir/esl_quicksort.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_quicksort.c.o -MF CMakeFiles/easel.dir/esl_quicksort.c.o.d -o CMakeFiles/easel.dir/esl_quicksort.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_quicksort.c [ 34%] Building C object ext/easel/CMakeFiles/easel.dir/esl_random.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_random.c.o -MF CMakeFiles/easel.dir/esl_random.c.o.d -o CMakeFiles/easel.dir/esl_random.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_random.c [ 34%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_lpileup.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_lpileup.c.o -MF CMakeFiles/samtools.dir/bam_lpileup.c.o.d -o CMakeFiles/samtools.dir/bam_lpileup.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_lpileup.c [ 34%] Building C object ext/easel/CMakeFiles/easel.dir/esl_rand64.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_rand64.c.o -MF CMakeFiles/easel.dir/esl_rand64.c.o.d -o CMakeFiles/easel.dir/esl_rand64.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_rand64.c [ 34%] Building C object ext/bwa/CMakeFiles/bwa.dir/rope.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/rope.c.o -MF CMakeFiles/bwa.dir/rope.c.o.d -o CMakeFiles/bwa.dir/rope.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rope.c [ 34%] Building C object ext/easel/CMakeFiles/easel.dir/esl_randomseq.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_randomseq.c.o -MF CMakeFiles/easel.dir/esl_randomseq.c.o.d -o CMakeFiles/easel.dir/esl_randomseq.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_randomseq.c [ 34%] Building C object ext/bwa/CMakeFiles/bwa.dir/rle.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/rle.c.o -MF CMakeFiles/bwa.dir/rle.c.o.d -o CMakeFiles/bwa.dir/rle.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rle.c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rope.c: In function 'rope_restore_node': /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rope.c:282:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 282 | fread(&is_bottom, 1, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rope.c:283:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 283 | fread(&n, 2, 1, fp); | ^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rope.c:291:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 291 | fread(p[i].c, 8, 6, fp); | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rope.c:292:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 292 | fread(q, 2, 1, fp); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rope.c:293:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 293 | fread(q + 1, 1, *q, fp); | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rope.c: In function 'rope_restore': /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rope.c:312:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 312 | fread(&r->max_nodes, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rope.c:313:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 313 | fread(&r->block_len, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 34%] Building C object ext/bwa/CMakeFiles/bwa.dir/kstring.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/kstring.c.o -MF CMakeFiles/bwa.dir/kstring.c.o.d -o CMakeFiles/bwa.dir/kstring.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/kstring.c [ 34%] Building C object ext/easel/CMakeFiles/easel.dir/esl_ratematrix.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_ratematrix.c.o -MF CMakeFiles/easel.dir/esl_ratematrix.c.o.d -o CMakeFiles/easel.dir/esl_ratematrix.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_ratematrix.c /usr/bin/ar qc libutils.a CMakeFiles/utils.dir/memory_limit.cpp.o CMakeFiles/utils.dir/filesystem/path_helper.cpp.o CMakeFiles/utils.dir/filesystem/temporary.cpp.o CMakeFiles/utils.dir/filesystem/glob.cpp.o CMakeFiles/utils.dir/logger/logger_impl.cpp.o CMakeFiles/utils.dir/logger/log_writers.cpp.o CMakeFiles/utils.dir/logger/log_writers_thread.cpp.o "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" /usr/bin/ranlib libutils.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 34%] Built target utils make -f common/io/graph/CMakeFiles/graphio.dir/build.make common/io/graph/CMakeFiles/graphio.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/graph /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/graph/CMakeFiles/graphio.dir/DependInfo.cmake "--color=" [ 34%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_md.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_md.c.o -MF CMakeFiles/samtools.dir/bam_md.c.o.d -o CMakeFiles/samtools.dir/bam_md.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_md.c make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/io/graph/CMakeFiles/graphio.dir/build.make common/io/graph/CMakeFiles/graphio.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 34%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/gfa.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/graph/CMakeFiles/graphio.dir/gfa.cpp.o -MF CMakeFiles/graphio.dir/gfa.cpp.o.d -o CMakeFiles/graphio.dir/gfa.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp [ 34%] Building C object ext/easel/CMakeFiles/easel.dir/esl_recorder.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_recorder.c.o -MF CMakeFiles/easel.dir/esl_recorder.c.o.d -o CMakeFiles/easel.dir/esl_recorder.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_recorder.c [ 35%] Building C object ext/easel/CMakeFiles/easel.dir/esl_red_black.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_red_black.c.o -MF CMakeFiles/easel.dir/esl_red_black.c.o.d -o CMakeFiles/easel.dir/esl_red_black.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_red_black.c [ 36%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/gfa_reader.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/graph/CMakeFiles/graphio.dir/gfa_reader.cpp.o -MF CMakeFiles/graphio.dir/gfa_reader.cpp.o.d -o CMakeFiles/graphio.dir/gfa_reader.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa_reader.cpp [ 36%] Building C object ext/samtools/CMakeFiles/samtools.dir/bgzf.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bgzf.c.o -MF CMakeFiles/samtools.dir/bgzf.c.o.d -o CMakeFiles/samtools.dir/bgzf.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bgzf.c [ 36%] Building C object ext/easel/CMakeFiles/easel.dir/esl_regexp.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_regexp.c.o -MF CMakeFiles/easel.dir/esl_regexp.c.o.d -o CMakeFiles/easel.dir/esl_regexp.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_regexp.c [ 36%] Building C object ext/samtools/CMakeFiles/samtools.dir/razf.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/razf.c.o -MF CMakeFiles/samtools.dir/razf.c.o.d -o CMakeFiles/samtools.dir/razf.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c [ 36%] Building C object ext/easel/CMakeFiles/easel.dir/esl_rootfinder.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_rootfinder.c.o -MF CMakeFiles/easel.dir/esl_rootfinder.c.o.d -o CMakeFiles/easel.dir/esl_rootfinder.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_rootfinder.c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c: In function 'razf_flush': /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c:221:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 221 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c:234:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 234 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c: In function '_razf_write': /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c:201:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 201 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c: In function 'razf_close': /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c:804:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 804 | write(rz->x.fpw, &rz->in, sizeof(int64_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c:805:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 805 | write(rz->x.fpw, &rz->out, sizeof(int64_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c:808:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 808 | write(rz->x.fpw, &v64, sizeof(int64_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c:810:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 810 | write(rz->x.fpw, &v64, sizeof(int64_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c: In function 'razf_end_flush': /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c:258:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 258 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c: In function 'save_zindex': /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c:96:19: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 96 | if(is_be) write(fd, &rz->index->size, sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c:99:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 99 | write(fd, &v32, sizeof(uint32_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c:106:9: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 106 | write(fd, rz->index->bin_offsets, sizeof(int64_t) * v32); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c:107:9: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 107 | write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 36%] Building C object ext/easel/CMakeFiles/easel.dir/esl_scorematrix.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_scorematrix.c.o -MF CMakeFiles/easel.dir/esl_scorematrix.c.o.d -o CMakeFiles/easel.dir/esl_scorematrix.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_scorematrix.c [ 36%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sqio.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sqio.c.o -MF CMakeFiles/easel.dir/esl_sqio.c.o.d -o CMakeFiles/easel.dir/esl_sqio.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_sqio.c [ 36%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sq.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sq.c.o -MF CMakeFiles/easel.dir/esl_sq.c.o.d -o CMakeFiles/easel.dir/esl_sq.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_sq.c [ 37%] Building C object ext/samtools/CMakeFiles/samtools.dir/bedidx.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bedidx.c.o -MF CMakeFiles/samtools.dir/bedidx.c.o.d -o CMakeFiles/samtools.dir/bedidx.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bedidx.c [ 37%] Building C object ext/samtools/CMakeFiles/samtools.dir/faidx.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/faidx.c.o -MF CMakeFiles/samtools.dir/faidx.c.o.d -o CMakeFiles/samtools.dir/faidx.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/faidx.c [ 37%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_sort.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_sort.c.o -MF CMakeFiles/samtools.dir/bam_sort.c.o.d -o CMakeFiles/samtools.dir/bam_sort.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_sort.c In file included from /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_scorematrix.c:22: /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_scorematrix.c: In function 'esl_scorematrix_Create': /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/easel.h:179:17: warning: argument 1 range [18446744071562067969, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 179 | if ( ((p) = malloc(size)) == NULL) { \ | ^~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_scorematrix.c:71:3: note: in expansion of macro 'ESL_ALLOC' 71 | ESL_ALLOC(S->outorder, sizeof(char) * (abc->Kp+1)); | ^~~~~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/easel.h:21: /usr/include/stdlib.h:672:14: note: in a call to allocation function 'malloc' declared here 672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^~~~~~ [ 39%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sqio_ascii.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sqio_ascii.c.o -MF CMakeFiles/easel.dir/esl_sqio_ascii.c.o.d -o CMakeFiles/easel.dir/esl_sqio_ascii.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_sqio_ascii.c [ 39%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sqio_ncbi.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sqio_ncbi.c.o -MF CMakeFiles/easel.dir/esl_sqio_ncbi.c.o.d -o CMakeFiles/easel.dir/esl_sqio_ncbi.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_sqio_ncbi.c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp: In lambda function: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:69:77: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] 69 | auto exponent = exp_char >> (dsl::lit_c<'+'> | dsl::lit_c<'-'>) + dsl::digits<>; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:74:40: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] 71 | dsl::position + | ~~~~~~~~~~~~~~~ 72 | integer + | ~~~~~~~~~ 73 | dsl::if_(fraction) + | ~~~~~~~~~~~~~~~~~~~~ 74 | dsl::if_(exponent) + | ~~~~~~~~~~~~~~~~~~~^ 75 | dsl::position; | ~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp: In lambda function: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:94:50: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] 94 | dsl::capture(LEXY_LIT("A")) >> colon + dsl::p | | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:95:50: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] 95 | dsl::capture(LEXY_LIT("i")) >> colon + dsl::p | | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:96:50: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] 96 | dsl::capture(LEXY_LIT("f")) >> colon + dsl::p | | ~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:97:50: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] 97 | dsl::capture(LEXY_LIT("Z")) >> colon + dsl::p | | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:98:50: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] 98 | dsl::capture(LEXY_LIT("J")) >> colon + dsl::p | | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:99:50: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] 99 | dsl::capture(LEXY_LIT("H")) >> colon + dsl::p | | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:100:50: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] 100 | dsl::capture(LEXY_LIT("B")) >> colon + dsl::p | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp: In lambda function: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:162:40: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] 162 | return dsl::eof | (tab >> tags + dsl::eof); | ~~~~~^~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp: At global scope: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:191:56: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] 189 | tab + dsl::p + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 190 | tab + (LEXY_LIT("*") | | ~~~~~~~~~~~~~~~~~~~~~~ 191 | dsl::identifier(dsl::ascii::alpha)) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 192 | dsl::p; | ~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:216:58: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] 212 | tab + dsl::p + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 213 | tab + dsl::p + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 214 | tab + dsl::p + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 215 | tab + dsl::p + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 216 | tab + (LEXY_LIT("*") | dsl::p) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 217 | dsl::p; | ~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:246:54: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] 244 | tab + dsl::p + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 245 | tab + dsl::p + | ~~~~~~~~~~~~~~~~~~~~~~~~ 246 | tab + (LEXY_LIT("*") | dsl::p) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 247 | dsl::p; | ~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp: In lambda function: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:269:41: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] 269 | dsl::ascii::alpha >> tab + dsl::until(dsl::newline).or_eof() | | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 39%] Building C object ext/easel/CMakeFiles/easel.dir/esl_ssi.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_ssi.c.o -MF CMakeFiles/easel.dir/esl_ssi.c.o.d -o CMakeFiles/easel.dir/esl_ssi.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_ssi.c [ 39%] Building C object ext/samtools/CMakeFiles/samtools.dir/sam_header.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/sam_header.c.o -MF CMakeFiles/samtools.dir/sam_header.c.o.d -o CMakeFiles/samtools.dir/sam_header.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/sam_header.c [ 39%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_reheader.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_reheader.c.o -MF CMakeFiles/samtools.dir/bam_reheader.c.o.d -o CMakeFiles/samtools.dir/bam_reheader.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_reheader.c [ 39%] Building C object ext/samtools/CMakeFiles/samtools.dir/kprobaln.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/kprobaln.c.o -MF CMakeFiles/samtools.dir/kprobaln.c.o.d -o CMakeFiles/samtools.dir/kprobaln.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/kprobaln.c [ 39%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Atomic.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Atomic.cpp.o -MF CMakeFiles/llvm-support.dir/Atomic.cpp.o.d -o CMakeFiles/llvm-support.dir/Atomic.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Atomic.cpp [ 39%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stack.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_stack.c.o -MF CMakeFiles/easel.dir/esl_stack.c.o.d -o CMakeFiles/easel.dir/esl_stack.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_stack.c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp: In instantiation of 'gfa::grammar::cigar_string::cigarop:: [with auto:48 = lexy::lexeme; uint32_t = unsigned int]': /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/include/lexy/callback/base.hpp:19:60: required by substitution of 'template using lexy::_detect_callback_for = decltype (declval()((declval)()...)) [with T = lexy::_callback >; Args = {unsigned int&, lexy::lexeme&&}]' 19 | using _detect_callback_for = decltype(LEXY_DECLVAL(const T)(LEXY_DECLVAL(Args)...)); | ^ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/include/lexy/_detail/detect.hpp:28:60: required from 'constexpr const bool lexy::_detail::is_detected using lexy::_detect_callback_for = decltype (declval()((declval)()...)), lexy::_callback >, unsigned int&, lexy::lexeme&&>' 28 | constexpr bool is_detected = _detector::value; | ^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/include/lexy/callback/base.hpp:22:16: required from 'constexpr const bool lexy::is_callback_for >, unsigned int&, lexy::lexeme&&>' 22 | = _detail::is_detected<_detect_callback_for, std::decay_t, Args...>; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/include/lexy/grammar.hpp:353:34: required from 'constexpr lexy::production_value_callback::return_type lexy::production_value_callback::operator()(Args&& ...) const [with Args = {unsigned int&, lexy::lexeme}; Production = gfa::grammar::cigar_string::cigarop; ParseState = void; return_type = gfa::cigarop]' 353 | else if constexpr (lexy::is_callback_for<_type, Args&&...>) | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/include/lexy/_detail/lazy_init.hpp:130:36: [ skipping 30 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/include/lexy/dsl/choice.hpp:108:60: required from 'lexyd::_chc, lexyd::_prd, lexyd::_prd, lexyd::_prd, lexyd::_br, lexyd::_until_eof >, lexyd::_br, lexyd::_until_eof >, lexyd::_err >::p::parse, void, gfa::grammar::record, void>, lexy::_prd>(lexy::_pc, void, gfa::grammar::record, void>&, lexy::_prd&):: [with auto:42 = lexyd::_prd::bp]' 108 | result = parser.template finish(context, reader, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 109 | static_cast(args)...); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/include/lexy/dsl/choice.hpp:114:39: required from 'static constexpr bool lexyd::_chc::p::parse(Context&, Reader&, Args&& ...) [with Context = lexy::_pc, void, gfa::grammar::record, void>; Reader = lexy::_prd; Args = {}; NextParser = lexy::_detail::final_parser; R = {lexyd::_prd, lexyd::_prd, lexyd::_prd, lexyd::_prd, lexyd::_br, lexyd::_until_eof >, lexyd::_br, lexyd::_until_eof >, lexyd::_err}]' 114 | auto found_branch = (try_r(lexy::branch_parser_for{}) || ...); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/include/lexy/action/base.hpp:210:37: required from 'constexpr auto lexy::_do_action(_pc&, Reader&) [with Handler = _ph<_prd>; State = void; Production = gfa::grammar::record; Reader = _prd; typename std::conditional<_production_defines_whitespace, Production, void>::type = void]' 210 | auto rule_result = parser::parse(context, reader); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/include/lexy/action/base.hpp:236:34: required from 'constexpr auto lexy::do_action(Handler&&, State*, Reader&) [with Production = gfa::grammar::record; Result = parse_action, lexy_ext::_report_error >::result_type; Handler = _ph<_prd>; State = void; Reader = _prd]' 236 | auto rule_result = _do_action(context, reader); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/include/lexy/action/parse.hpp:164:56: required from 'constexpr auto lexy::parse_action::operator()(Production, const Input&) const [with Production = gfa::grammar::record; State = void; Input = lexy::string_input; ErrorCallback = lexy_ext::_report_error]' 164 | return lexy::do_action(handler(input_holder, sink), _state, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 165 | reader); | ~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/include/lexy/action/parse.hpp:173:62: required from 'constexpr auto lexy::parse(const Input&, const ErrorCallback&) [with Production = gfa::grammar::record; Input = string_input; ErrorCallback = lexy_ext::_report_error]' 173 | return parse_action(callback)(Production{}, input); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:280:47: required from here 280 | auto result = lexy::parse(lexy::string_input(line, len), lexy_ext::report_error); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:151:37: warning: conversion from 'uint32_t' {aka 'unsigned int'} to 'unsigned int:24' may change value [-Wconversion] 151 | return gfa::cigarop{cnt, lexeme[0]}; | ^~~ [ 39%] Building C object ext/samtools/CMakeFiles/samtools.dir/knetfile.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/knetfile.c.o -MF CMakeFiles/samtools.dir/knetfile.c.o.d -o CMakeFiles/samtools.dir/knetfile.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/knetfile.c In file included from /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/knetfile.c:46: /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/knetfile.c: In function 'kftp_send_cmd': /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/knetfile.h:9:32: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) | ^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/knetfile.c:236:9: note: in expansion of macro 'netwrite' 236 | netwrite(ftp->ctrl_fd, cmd, strlen(cmd)); | ^~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/knetfile.c: In function 'khttp_connect_file': /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/knetfile.h:9:32: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) | ^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/knetfile.c:415:9: note: in expansion of macro 'netwrite' 415 | netwrite(fp->fd, buf, l); | ^~~~~~~~ [ 40%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_cat.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_cat.c.o -MF CMakeFiles/samtools.dir/bam_cat.c.o.d -o CMakeFiles/samtools.dir/bam_cat.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_cat.c [ 40%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o -MF CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o.d -o CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/CrashRecoveryContext.cpp [ 40%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Debug.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Debug.cpp.o -MF CMakeFiles/llvm-support.dir/Debug.cpp.o.d -o CMakeFiles/llvm-support.dir/Debug.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Debug.cpp [ 40%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stats.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_stats.c.o -MF CMakeFiles/easel.dir/esl_stats.c.o.d -o CMakeFiles/easel.dir/esl_stats.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_stats.c [ 40%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Errno.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Errno.cpp.o -MF CMakeFiles/llvm-support.dir/Errno.cpp.o.d -o CMakeFiles/llvm-support.dir/Errno.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Errno.cpp [ 41%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Error.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Error.cpp.o -MF CMakeFiles/llvm-support.dir/Error.cpp.o.d -o CMakeFiles/llvm-support.dir/Error.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Error.cpp [ 41%] Linking C static library libsamtools.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cmake -P CMakeFiles/samtools.dir/cmake_clean_target.cmake [ 41%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stopwatch.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_stopwatch.c.o -MF CMakeFiles/easel.dir/esl_stopwatch.c.o.d -o CMakeFiles/easel.dir/esl_stopwatch.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_stopwatch.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cmake -E cmake_link_script CMakeFiles/samtools.dir/link.txt --verbose=1 /usr/bin/ar qc libsamtools.a CMakeFiles/samtools.dir/kstring.c.o CMakeFiles/samtools.dir/bam_aux.c.o CMakeFiles/samtools.dir/bam.c.o CMakeFiles/samtools.dir/bam_import.c.o CMakeFiles/samtools.dir/sam.c.o CMakeFiles/samtools.dir/bam_index.c.o CMakeFiles/samtools.dir/bam_pileup.c.o CMakeFiles/samtools.dir/bam_lpileup.c.o CMakeFiles/samtools.dir/bam_md.c.o CMakeFiles/samtools.dir/bgzf.c.o CMakeFiles/samtools.dir/razf.c.o CMakeFiles/samtools.dir/faidx.c.o CMakeFiles/samtools.dir/bedidx.c.o CMakeFiles/samtools.dir/bam_sort.c.o CMakeFiles/samtools.dir/sam_header.c.o CMakeFiles/samtools.dir/bam_reheader.c.o CMakeFiles/samtools.dir/kprobaln.c.o CMakeFiles/samtools.dir/knetfile.c.o CMakeFiles/samtools.dir/bam_cat.c.o /usr/bin/ranlib libsamtools.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 41%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o -MF CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o.d -o CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/ErrorHandling.cpp [ 41%] Built target samtools [ 42%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stretchexp.c.o make -f common/io/sam/CMakeFiles/samio.dir/build.make common/io/sam/CMakeFiles/samio.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/sam /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/sam /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/sam/CMakeFiles/samio.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_stretchexp.c.o -MF CMakeFiles/easel.dir/esl_stretchexp.c.o.d -o CMakeFiles/easel.dir/esl_stretchexp.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_stretchexp.c make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 42%] Building C object ext/easel/CMakeFiles/easel.dir/esl_subcmd.c.o make -f common/io/sam/CMakeFiles/samio.dir/build.make common/io/sam/CMakeFiles/samio.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_subcmd.c.o -MF CMakeFiles/easel.dir/esl_subcmd.c.o.d -o CMakeFiles/easel.dir/esl_subcmd.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_subcmd.c [ 42%] Building CXX object common/io/sam/CMakeFiles/samio.dir/read.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/sam && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/sam -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/sam/CMakeFiles/samio.dir/read.cpp.o -MF CMakeFiles/samio.dir/read.cpp.o.d -o CMakeFiles/samio.dir/read.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/sam/read.cpp [ 43%] Linking C static library libbwa.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cmake -P CMakeFiles/bwa.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cmake -E cmake_link_script CMakeFiles/bwa.dir/link.txt --verbose=1 [ 43%] Building C object ext/easel/CMakeFiles/easel.dir/esl_threads.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_threads.c.o -MF CMakeFiles/easel.dir/esl_threads.c.o.d -o CMakeFiles/easel.dir/esl_threads.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_threads.c /usr/bin/ar qc libbwa.a CMakeFiles/bwa.dir/utils.c.o CMakeFiles/bwa.dir/kthread.c.o CMakeFiles/bwa.dir/ksw.c.o CMakeFiles/bwa.dir/bwt.c.o CMakeFiles/bwa.dir/bntseq.c.o CMakeFiles/bwa.dir/bwa.c.o CMakeFiles/bwa.dir/bwamem.c.o CMakeFiles/bwa.dir/bwamem_pair.c.o CMakeFiles/bwa.dir/bwamem_extra.c.o CMakeFiles/bwa.dir/malloc_wrap.c.o CMakeFiles/bwa.dir/is.c.o CMakeFiles/bwa.dir/bwtindex.c.o CMakeFiles/bwa.dir/rope.c.o CMakeFiles/bwa.dir/rle.c.o CMakeFiles/bwa.dir/kstring.c.o /usr/bin/ranlib libbwa.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 43%] Built target bwa make -f ext/bwa/CMakeFiles/spades-bwa.dir/build.make ext/bwa/CMakeFiles/spades-bwa.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa/CMakeFiles/spades-bwa.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f ext/bwa/CMakeFiles/spades-bwa.dir/build.make ext/bwa/CMakeFiles/spades-bwa.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 43%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/main.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/main.c.o -MF CMakeFiles/spades-bwa.dir/main.c.o.d -o CMakeFiles/spades-bwa.dir/main.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/main.c [ 43%] Building C object ext/easel/CMakeFiles/easel.dir/esl_varint.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_varint.c.o -MF CMakeFiles/easel.dir/esl_varint.c.o.d -o CMakeFiles/easel.dir/esl_varint.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_varint.c [ 43%] Building C object ext/easel/CMakeFiles/easel.dir/esl_tree.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_tree.c.o -MF CMakeFiles/easel.dir/esl_tree.c.o.d -o CMakeFiles/easel.dir/esl_tree.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_tree.c [ 43%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/fastmap.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/fastmap.c.o -MF CMakeFiles/spades-bwa.dir/fastmap.c.o.d -o CMakeFiles/spades-bwa.dir/fastmap.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/fastmap.c [ 43%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/FoldingSet.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/FoldingSet.cpp.o -MF CMakeFiles/llvm-support.dir/FoldingSet.cpp.o.d -o CMakeFiles/llvm-support.dir/FoldingSet.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/FoldingSet.cpp [ 43%] Building C object ext/easel/CMakeFiles/easel.dir/esl_vectorops.c.o [ 43%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_vectorops.c.o -MF CMakeFiles/easel.dir/esl_vectorops.c.o.d -o CMakeFiles/easel.dir/esl_vectorops.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_vectorops.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o -MF CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o.d -o CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/FormatVariadic.cpp [ 43%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Hashing.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Hashing.cpp.o -MF CMakeFiles/llvm-support.dir/Hashing.cpp.o.d -o CMakeFiles/llvm-support.dir/Hashing.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Hashing.cpp [ 43%] Building CXX object common/io/sam/CMakeFiles/samio.dir/sam_reader.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/sam && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/sam -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/sam/CMakeFiles/samio.dir/sam_reader.cpp.o -MF CMakeFiles/samio.dir/sam_reader.cpp.o.d -o CMakeFiles/samio.dir/sam_reader.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/sam/sam_reader.cpp [ 43%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/pemerge.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/pemerge.c.o -MF CMakeFiles/spades-bwa.dir/pemerge.c.o.d -o CMakeFiles/spades-bwa.dir/pemerge.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/pemerge.c In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa_reader.cpp:12: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/construction_helper.hpp: In instantiation of 'void omnigraph::ConstructionHelper::DeleteLink(VertexId, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster; VertexId = omnigraph::impl::VertexId; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/construction_helper.hpp:108:13: required from 'void omnigraph::ConstructionHelper::LinkEdges(EdgeId, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster; EdgeId = omnigraph::impl::EdgeId]' 108 | DeleteLink(graph_.conjugate(w), graph_.conjugate(in_edge)); | ^~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa_reader.cpp:185:25: required from here 185 | helper.LinkEdges(e1, e2); | ~~~~~~~~~~~~~~~~^~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/construction_helper.hpp:118:14: warning: unused variable 'res' [-Wunused-variable] 118 | bool res = graph_.vertex(v).RemoveOutgoingEdge(e); | ^~~ [ 43%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Host.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Host.cpp.o -MF CMakeFiles/llvm-support.dir/Host.cpp.o.d -o CMakeFiles/llvm-support.dir/Host.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Host.cpp [ 45%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/JSON.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/JSON.cpp.o -MF CMakeFiles/llvm-support.dir/JSON.cpp.o.d -o CMakeFiles/llvm-support.dir/JSON.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/JSON.cpp [ 45%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/maxk.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/maxk.c.o -MF CMakeFiles/spades-bwa.dir/maxk.c.o.d -o CMakeFiles/spades-bwa.dir/maxk.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/maxk.c [ 46%] Building C object ext/easel/CMakeFiles/easel.dir/esl_weibull.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_weibull.c.o -MF CMakeFiles/easel.dir/esl_weibull.c.o.d -o CMakeFiles/easel.dir/esl_weibull.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_weibull.c [ 47%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/kopen.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/kopen.c.o -MF CMakeFiles/spades-bwa.dir/kopen.c.o.d -o CMakeFiles/spades-bwa.dir/kopen.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/kopen.c [ 47%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/LEB128.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/LEB128.cpp.o -MF CMakeFiles/llvm-support.dir/LEB128.cpp.o.d -o CMakeFiles/llvm-support.dir/LEB128.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/LEB128.cpp In file included from /usr/include/string.h:548, from /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/kopen.c:6: In function 'strncpy', inlined from 'cmd2argv' at /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/kopen.c:246:2, inlined from 'kopen' at /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/kopen.c:307:13: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:100:10: warning: '__builtin_strncpy' specified bound between 18446744071562067969 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 100 | return __builtin___strncpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 101 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'cmd2argv', inlined from 'kopen' at /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/kopen.c:307:13: /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/kopen.c:245:32: warning: argument 1 range [18446744071562067970, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 245 | argv[0] = str = (char*)calloc(end - beg + 1, 1); | ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/kopen.c:7: /usr/include/stdlib.h: In function 'kopen': /usr/include/stdlib.h:675:14: note: in a call to allocation function 'calloc' declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ [ 47%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwtaln.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/bwtaln.c.o -MF CMakeFiles/spades-bwa.dir/bwtaln.c.o.d -o CMakeFiles/spades-bwa.dir/bwtaln.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwtaln.c [ 47%] Building C object ext/easel/CMakeFiles/easel.dir/esl_workqueue.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_workqueue.c.o -MF CMakeFiles/easel.dir/esl_workqueue.c.o.d -o CMakeFiles/easel.dir/esl_workqueue.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_workqueue.c [ 47%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/LineIterator.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/LineIterator.cpp.o -MF CMakeFiles/llvm-support.dir/LineIterator.cpp.o.d -o CMakeFiles/llvm-support.dir/LineIterator.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/LineIterator.cpp [ 47%] Building C object ext/easel/CMakeFiles/easel.dir/esl_wuss.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_wuss.c.o -MF CMakeFiles/easel.dir/esl_wuss.c.o.d -o CMakeFiles/easel.dir/esl_wuss.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_wuss.c [ 47%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Locale.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Locale.cpp.o -MF CMakeFiles/llvm-support.dir/Locale.cpp.o.d -o CMakeFiles/llvm-support.dir/Locale.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Locale.cpp [ 47%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwtgap.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/bwtgap.c.o -MF CMakeFiles/spades-bwa.dir/bwtgap.c.o.d -o CMakeFiles/spades-bwa.dir/bwtgap.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwtgap.c [ 47%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sse.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sse.c.o -MF CMakeFiles/easel.dir/esl_sse.c.o.d -o CMakeFiles/easel.dir/esl_sse.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_sse.c [ 47%] Building C object ext/easel/CMakeFiles/easel.dir/esl_avx.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_avx.c.o -MF CMakeFiles/easel.dir/esl_avx.c.o.d -o CMakeFiles/easel.dir/esl_avx.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_avx.c [ 47%] Building C object ext/easel/CMakeFiles/easel.dir/esl_avx512.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_avx512.c.o -MF CMakeFiles/easel.dir/esl_avx512.c.o.d -o CMakeFiles/easel.dir/esl_avx512.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_avx512.c [ 47%] Building CXX object common/io/sam/CMakeFiles/samio.dir/bam_parser.cpp.o [ 47%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwaseqio.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/sam && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/sam -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/sam/CMakeFiles/samio.dir/bam_parser.cpp.o -MF CMakeFiles/samio.dir/bam_parser.cpp.o.d -o CMakeFiles/samio.dir/bam_parser.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/sam/bam_parser.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/bwaseqio.c.o -MF CMakeFiles/spades-bwa.dir/bwaseqio.c.o.d -o CMakeFiles/spades-bwa.dir/bwaseqio.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwaseqio.c [ 47%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/MD5.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/MD5.cpp.o -MF CMakeFiles/llvm-support.dir/MD5.cpp.o.d -o CMakeFiles/llvm-support.dir/MD5.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/MD5.cpp [ 48%] Building C object ext/easel/CMakeFiles/easel.dir/esl_neon.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_neon.c.o -MF CMakeFiles/easel.dir/esl_neon.c.o.d -o CMakeFiles/easel.dir/esl_neon.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_neon.c [ 48%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o -MF CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o.d -o CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/ManagedStatic.cpp [ 48%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/gfa_writer.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/graph/CMakeFiles/graphio.dir/gfa_writer.cpp.o -MF CMakeFiles/graphio.dir/gfa_writer.cpp.o.d -o CMakeFiles/graphio.dir/gfa_writer.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa_writer.cpp [ 50%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/MemAlloc.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/MemAlloc.cpp.o -MF CMakeFiles/llvm-support.dir/MemAlloc.cpp.o.d -o CMakeFiles/llvm-support.dir/MemAlloc.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/MemAlloc.cpp [ 50%] Linking C static library libeasel.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cmake -P CMakeFiles/easel.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cmake -E cmake_link_script CMakeFiles/easel.dir/link.txt --verbose=1 [ 50%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bamlite.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/bamlite.c.o -MF CMakeFiles/spades-bwa.dir/bamlite.c.o.d -o CMakeFiles/spades-bwa.dir/bamlite.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bamlite.c [ 50%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o -MF CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o.d -o CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/MemoryBuffer.cpp [ 51%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwtsw2_main.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/bwtsw2_main.c.o -MF CMakeFiles/spades-bwa.dir/bwtsw2_main.c.o.d -o CMakeFiles/spades-bwa.dir/bwtsw2_main.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwtsw2_main.c /usr/bin/ar qc libeasel.a CMakeFiles/easel.dir/easel.c.o CMakeFiles/easel.dir/esl_alloc.c.o CMakeFiles/easel.dir/esl_alphabet.c.o CMakeFiles/easel.dir/esl_arr2.c.o CMakeFiles/easel.dir/esl_arr3.c.o CMakeFiles/easel.dir/esl_bitfield.c.o CMakeFiles/easel.dir/esl_buffer.c.o CMakeFiles/easel.dir/esl_cluster.c.o CMakeFiles/easel.dir/esl_composition.c.o CMakeFiles/easel.dir/esl_cpu.c.o CMakeFiles/easel.dir/esl_dirichlet.c.o 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CMakeFiles/easel.dir/esl_sqio.c.o CMakeFiles/easel.dir/esl_sqio_ascii.c.o CMakeFiles/easel.dir/esl_sqio_ncbi.c.o CMakeFiles/easel.dir/esl_ssi.c.o CMakeFiles/easel.dir/esl_stack.c.o CMakeFiles/easel.dir/esl_stats.c.o CMakeFiles/easel.dir/esl_stopwatch.c.o CMakeFiles/easel.dir/esl_stretchexp.c.o CMakeFiles/easel.dir/esl_subcmd.c.o CMakeFiles/easel.dir/esl_threads.c.o CMakeFiles/easel.dir/esl_tree.c.o CMakeFiles/easel.dir/esl_varint.c.o CMakeFiles/easel.dir/esl_vectorops.c.o CMakeFiles/easel.dir/esl_weibull.c.o CMakeFiles/easel.dir/esl_workqueue.c.o CMakeFiles/easel.dir/esl_wuss.c.o CMakeFiles/easel.dir/esl_sse.c.o CMakeFiles/easel.dir/esl_avx.c.o CMakeFiles/easel.dir/esl_avx512.c.o CMakeFiles/easel.dir/esl_neon.c.o /usr/bin/ranlib libeasel.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 51%] Built target easel make -f ext/hmmer/CMakeFiles/hmmer.dir/build.make ext/hmmer/CMakeFiles/hmmer.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/CMakeFiles/hmmer.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f ext/hmmer/CMakeFiles/hmmer.dir/build.make ext/hmmer/CMakeFiles/hmmer.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 51%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwashm.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/bwashm.c.o -MF CMakeFiles/spades-bwa.dir/bwashm.c.o.d -o CMakeFiles/spades-bwa.dir/bwashm.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwashm.c [ 51%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/build.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/build.c.o -MF CMakeFiles/hmmer.dir/src/build.c.o.d -o CMakeFiles/hmmer.dir/src/build.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/build.c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwashm.c: In function 'bwa_shm_stage': /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwashm.c:29:9: warning: ignoring return value of 'ftruncate' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | ftruncate(shmid, BWA_CTL_SIZE); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwashm.c:66:9: warning: ignoring return value of 'ftruncate' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | ftruncate(shmid, idx->l_mem); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 51%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp 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-ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Path.cpp.o -MF CMakeFiles/llvm-support.dir/Path.cpp.o.d -o CMakeFiles/llvm-support.dir/Path.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Path.cpp [ 51%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/cachedb.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/cachedb.c.o -MF CMakeFiles/hmmer.dir/src/cachedb.c.o.d -o CMakeFiles/hmmer.dir/src/cachedb.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/cachedb.c [ 51%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwtsw2_aux.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/bwtsw2_aux.c.o -MF CMakeFiles/spades-bwa.dir/bwtsw2_aux.c.o.d -o CMakeFiles/spades-bwa.dir/bwtsw2_aux.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwtsw2_aux.c [ 51%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Process.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Process.cpp.o -MF CMakeFiles/llvm-support.dir/Process.cpp.o.d -o CMakeFiles/llvm-support.dir/Process.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Process.cpp [ 52%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/emit.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem 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-I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/errors.c.o -MF CMakeFiles/hmmer.dir/src/errors.c.o.d -o CMakeFiles/hmmer.dir/src/errors.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/errors.c [ 52%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/evalues.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/evalues.c.o -MF CMakeFiles/hmmer.dir/src/evalues.c.o.d -o CMakeFiles/hmmer.dir/src/evalues.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/evalues.c [ 52%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/eweight.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/eweight.c.o -MF CMakeFiles/hmmer.dir/src/eweight.c.o.d -o CMakeFiles/hmmer.dir/src/eweight.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/eweight.c [ 52%] Linking CXX static library libsamio.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/sam && /usr/bin/cmake -P CMakeFiles/samio.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/sam && /usr/bin/cmake -E cmake_link_script CMakeFiles/samio.dir/link.txt --verbose=1 [ 52%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Program.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Program.cpp.o -MF CMakeFiles/llvm-support.dir/Program.cpp.o.d -o CMakeFiles/llvm-support.dir/Program.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Program.cpp /usr/bin/ar qc libsamio.a CMakeFiles/samio.dir/read.cpp.o CMakeFiles/samio.dir/sam_reader.cpp.o CMakeFiles/samio.dir/bam_parser.cpp.o /usr/bin/ranlib libsamio.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 52%] Built target samio [ 52%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_decoding.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/generic_decoding.c.o -MF CMakeFiles/hmmer.dir/src/generic_decoding.c.o.d -o CMakeFiles/hmmer.dir/src/generic_decoding.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/generic_decoding.c [ 53%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Regex.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Regex.cpp.o -MF CMakeFiles/llvm-support.dir/Regex.cpp.o.d -o CMakeFiles/llvm-support.dir/Regex.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Regex.cpp [ 53%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_fwdback.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/generic_fwdback.c.o -MF CMakeFiles/hmmer.dir/src/generic_fwdback.c.o.d -o CMakeFiles/hmmer.dir/src/generic_fwdback.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/generic_fwdback.c [ 53%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwtsw2_core.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/bwtsw2_core.c.o -MF CMakeFiles/spades-bwa.dir/bwtsw2_core.c.o.d -o CMakeFiles/spades-bwa.dir/bwtsw2_core.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwtsw2_core.c In file included from /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Process.cpp:100: /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Process.inc: In static member function 'static size_t llvm::sys::Process::GetMallocUsage()': /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Process.inc:94:18: warning: 'mallinfo mallinfo()' is deprecated [-Wdeprecated-declarations] 94 | mi = ::mallinfo(); | ~~~~~~~~~~^~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Process.inc:35: /usr/include/malloc.h:114:24: note: declared here 114 | extern struct mallinfo mallinfo (void) __THROW __MALLOC_DEPRECATED; | ^~~~~~~~ [ 53%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/fastg_writer.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/graph/CMakeFiles/graphio.dir/fastg_writer.cpp.o -MF CMakeFiles/graphio.dir/fastg_writer.cpp.o.d -o CMakeFiles/graphio.dir/fastg_writer.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/fastg_writer.cpp [ 54%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_fwdback_chk.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/generic_fwdback_chk.c.o -MF CMakeFiles/hmmer.dir/src/generic_fwdback_chk.c.o.d -o CMakeFiles/hmmer.dir/src/generic_fwdback_chk.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/generic_fwdback_chk.c [ 54%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Signals.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Signals.cpp.o -MF CMakeFiles/llvm-support.dir/Signals.cpp.o.d -o CMakeFiles/llvm-support.dir/Signals.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Signals.cpp [ 54%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_fwdback_banded.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/generic_fwdback_banded.c.o -MF CMakeFiles/hmmer.dir/src/generic_fwdback_banded.c.o.d -o CMakeFiles/hmmer.dir/src/generic_fwdback_banded.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/generic_fwdback_banded.c In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/string:43, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/stacktrace.hpp:18, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/verify.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/binary.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/io_base.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:10: In member function 'void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = phmap::priv::Deallocate<8, std::allocator > > > > >(std::allocator > > > >*, void*, size_t)::M]', inlined from 'static void phmap::allocator_traits::deallocate(Alloc&, pointer, size_type) [with Alloc = std::allocator > > > > >(std::allocator > > > >*, void*, size_t)::M>]' at /usr/include/parallel_hashmap/phmap_base.h:1487:21, inlined from 'void phmap::priv::Deallocate(Alloc*, void*, size_t) [with long unsigned int Alignment = 8; Alloc = std::allocator > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:4210:17, inlined from 'void phmap::priv::btree::deallocate(size_type, node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2003:60, inlined from 'void phmap::priv::btree::delete_leaf_node(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2013:23, inlined from 'void phmap::priv::btree::internal_clear(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:3228:29, inlined from 'void phmap::priv::btree::clear() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2859:27, inlined from 'phmap::priv::btree::~btree() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:1704:18, inlined from 'phmap::priv::btree_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_container()' at /usr/include/parallel_hashmap/btree.h:3264:11, inlined from 'phmap::priv::btree_set_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_set_container()' at /usr/include/parallel_hashmap/btree.h:3429:11, inlined from 'phmap::priv::btree_map_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_map_container()' at /usr/include/parallel_hashmap/btree.h:3591:11, inlined from 'phmap::btree_map > >, phmap::Less, std::allocator > > > > >::~btree_map()' at /usr/include/parallel_hashmap/btree.h:3952:15, inlined from 'omnigraph::de::NoLockingConstAdapter > >, phmap::Less, std::allocator > > > > > >::~NoLockingConstAdapter()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info.hpp:567:7, inlined from 'std::pair > >, phmap::Less, std::allocator > > > > > > >::~pair()' at /usr/include/c++/14/bits/stl_pair.h:284:12, inlined from 'void std::__new_allocator<_Tp>::destroy(_Up*) [with _Up = std::pair > >, phmap::Less, std::allocator > > > > > > >; _Tp = std::pair > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/c++/14/bits/new_allocator.h:198:13, inlined from 'static void std::allocator_traits >::destroy(allocator_type&, _Up*) [with _Up = std::pair > >, phmap::Less, std::allocator > > > > > > >; _Tp = std::pair > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/c++/14/bits/alloc_traits.h:597:15, inlined from 'static decltype (std::allocator_traits::destroy(a, p)) phmap::allocator_traits::destroy_impl(int, A&, T*) [with A = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; T = std::pair > >, phmap::Less, std::allocator > > > > > > >; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:1546:42, inlined from 'static void phmap::allocator_traits::destroy(Alloc&, T*) [with T = std::pair > >, phmap::Less, std::allocator > > > > > > >; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:1504:21, inlined from 'static void phmap::priv::map_slot_policy::swap(Allocator*, slot_type*, slot_type*) [with Allocator = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; K = omnigraph::impl::EdgeId; V = omnigraph::de::NoLockingConstAdapter > >, phmap::Less, std::allocator > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:4554:56, inlined from 'static void phmap::priv::common_params::swap(Alloc*, slot_type*, slot_type*) [with Key = omnigraph::impl::EdgeId; Compare = phmap::Less; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; int TargetNodeSize = 256; bool Multi = false; SlotPolicy = phmap::priv::map_slot_policy > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/parallel_hashmap/btree.h:888:30, inlined from 'void phmap::priv::btree_node::swap(phmap::priv::btree_node*, allocator_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > > > >, phmap::Less, std::allocator > >, phmap::Less, std::allocator > > > > > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2382:30: /usr/include/c++/14/bits/new_allocator.h:172:33: warning: 'void operator delete(void*, std::size_t)' called on unallocated object 'empty_node' [-Wfree-nonheap-object] 172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:15, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/observable_graph.hpp:13, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:12: /usr/include/parallel_hashmap/btree.h: In function 'void phmap::priv::btree_node::swap(phmap::priv::btree_node*, allocator_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > > > >, phmap::Less, std::allocator > >, phmap::Less, std::allocator > > > > > > > >, 256, false>]': /usr/include/parallel_hashmap/btree.h:1623:44: note: declared here 1623 | static constexpr EmptyNodeType empty_node( | ^~~~~~~~~~ [ 54%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_null2.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/generic_null2.c.o -MF CMakeFiles/hmmer.dir/src/generic_null2.c.o.d -o CMakeFiles/hmmer.dir/src/generic_null2.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/generic_null2.c [ 54%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_msv.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/generic_msv.c.o -MF CMakeFiles/hmmer.dir/src/generic_msv.c.o.d -o CMakeFiles/hmmer.dir/src/generic_msv.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/generic_msv.c [ 54%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_optacc.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/generic_optacc.c.o -MF CMakeFiles/hmmer.dir/src/generic_optacc.c.o.d -o CMakeFiles/hmmer.dir/src/generic_optacc.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/generic_optacc.c [ 54%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_stotrace.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/generic_stotrace.c.o -MF CMakeFiles/hmmer.dir/src/generic_stotrace.c.o.d -o CMakeFiles/hmmer.dir/src/generic_stotrace.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/generic_stotrace.c In member function 'void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = phmap::priv::Deallocate<8, std::allocator > > > > >(std::allocator > > > >*, void*, size_t)::M]', inlined from 'static void phmap::allocator_traits::deallocate(Alloc&, pointer, size_type) [with Alloc = std::allocator > > > > >(std::allocator > > > >*, void*, size_t)::M>]' at /usr/include/parallel_hashmap/phmap_base.h:1487:21, inlined from 'void phmap::priv::Deallocate(Alloc*, void*, size_t) [with long unsigned int Alignment = 8; Alloc = std::allocator > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:4210:17, inlined from 'void phmap::priv::btree::deallocate(size_type, node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2003:60, inlined from 'void phmap::priv::btree::delete_leaf_node(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2013:23, inlined from 'void phmap::priv::btree::internal_clear(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:3228:29, inlined from 'void phmap::priv::btree::clear() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2859:27, inlined from 'phmap::priv::btree::~btree() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:1704:18, inlined from 'phmap::priv::btree_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_container()' at /usr/include/parallel_hashmap/btree.h:3264:11, inlined from 'phmap::priv::btree_set_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_set_container()' at /usr/include/parallel_hashmap/btree.h:3429:11, inlined from 'phmap::priv::btree_map_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_map_container()' at /usr/include/parallel_hashmap/btree.h:3591:11, inlined from 'phmap::btree_map > >, phmap::Less, std::allocator > > > > >::~btree_map()' at /usr/include/parallel_hashmap/btree.h:3952:15, inlined from 'omnigraph::de::NoLockingAdapter > >, phmap::Less, std::allocator > > > > > >::~NoLockingAdapter()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info.hpp:536:7, inlined from 'std::pair > >, phmap::Less, std::allocator > > > > > > >::~pair()' at /usr/include/c++/14/bits/stl_pair.h:284:12, inlined from 'void std::__new_allocator<_Tp>::destroy(_Up*) [with _Up = std::pair > >, phmap::Less, std::allocator > > > > > > >; _Tp = std::pair > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/c++/14/bits/new_allocator.h:198:13, inlined from 'static void std::allocator_traits >::destroy(allocator_type&, _Up*) [with _Up = std::pair > >, phmap::Less, std::allocator > > > > > > >; _Tp = std::pair > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/c++/14/bits/alloc_traits.h:597:15, inlined from 'static decltype (std::allocator_traits::destroy(a, p)) phmap::allocator_traits::destroy_impl(int, A&, T*) [with A = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; T = std::pair > >, phmap::Less, std::allocator > > > > > > >; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:1546:42, inlined from 'static void phmap::allocator_traits::destroy(Alloc&, T*) [with T = std::pair > >, phmap::Less, std::allocator > > > > > > >; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:1504:21, inlined from 'static void phmap::priv::map_slot_policy::swap(Allocator*, slot_type*, slot_type*) [with Allocator = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; K = omnigraph::impl::EdgeId; V = omnigraph::de::NoLockingAdapter > >, phmap::Less, std::allocator > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:4554:56, inlined from 'static void phmap::priv::common_params::swap(Alloc*, slot_type*, slot_type*) [with Key = omnigraph::impl::EdgeId; Compare = phmap::Less; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; int TargetNodeSize = 256; bool Multi = false; SlotPolicy = phmap::priv::map_slot_policy > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/parallel_hashmap/btree.h:888:30, inlined from 'void phmap::priv::btree_node::swap(phmap::priv::btree_node*, allocator_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > > > >, phmap::Less, std::allocator > >, phmap::Less, std::allocator > > > > > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2382:30: /usr/include/c++/14/bits/new_allocator.h:172:33: warning: 'void operator delete(void*, std::size_t)' called on unallocated object 'empty_node' [-Wfree-nonheap-object] 172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ /usr/include/parallel_hashmap/btree.h: In function 'void phmap::priv::btree_node::swap(phmap::priv::btree_node*, allocator_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > > > >, phmap::Less, std::allocator > >, phmap::Less, std::allocator > > > > > > > >, 256, false>]': /usr/include/parallel_hashmap/btree.h:1623:44: note: declared here 1623 | static constexpr EmptyNodeType empty_node( | ^~~~~~~~~~ [ 56%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_viterbi.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/generic_viterbi.c.o -MF CMakeFiles/hmmer.dir/src/generic_viterbi.c.o.d -o CMakeFiles/hmmer.dir/src/generic_viterbi.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/generic_viterbi.c [ 56%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/SmallVector.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/SmallVector.cpp.o -MF CMakeFiles/llvm-support.dir/SmallVector.cpp.o.d -o CMakeFiles/llvm-support.dir/SmallVector.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/SmallVector.cpp [ 56%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwtsw2_chain.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/bwtsw2_chain.c.o -MF CMakeFiles/spades-bwa.dir/bwtsw2_chain.c.o.d -o CMakeFiles/spades-bwa.dir/bwtsw2_chain.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwtsw2_chain.c [ 56%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_vtrace.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/generic_vtrace.c.o -MF CMakeFiles/hmmer.dir/src/generic_vtrace.c.o.d -o CMakeFiles/hmmer.dir/src/generic_vtrace.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/generic_vtrace.c [ 56%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/h2_io.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/h2_io.c.o -MF CMakeFiles/hmmer.dir/src/h2_io.c.o.d -o CMakeFiles/hmmer.dir/src/h2_io.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/h2_io.c [ 56%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwt_lite.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/bwt_lite.c.o -MF CMakeFiles/spades-bwa.dir/bwt_lite.c.o.d -o CMakeFiles/spades-bwa.dir/bwt_lite.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwt_lite.c [ 56%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/heatmap.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/heatmap.c.o -MF CMakeFiles/hmmer.dir/src/heatmap.c.o.d -o CMakeFiles/hmmer.dir/src/heatmap.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/heatmap.c [ 56%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmlogo.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/hmmlogo.c.o -MF CMakeFiles/hmmer.dir/src/hmmlogo.c.o.d -o CMakeFiles/hmmer.dir/src/hmmlogo.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/hmmlogo.c [ 57%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwape.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/bwape.c.o -MF CMakeFiles/spades-bwa.dir/bwape.c.o.d -o CMakeFiles/spades-bwa.dir/bwape.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwape.c [ 57%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdmstr.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdmstr.c.o -MF CMakeFiles/hmmer.dir/src/hmmdmstr.c.o.d -o CMakeFiles/hmmer.dir/src/hmmdmstr.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/hmmdmstr.c [ 57%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwase.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/bwase.c.o -MF CMakeFiles/spades-bwa.dir/bwase.c.o.d -o CMakeFiles/spades-bwa.dir/bwase.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwase.c [ 57%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwtsw2_pair.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/bwtsw2_pair.c.o -MF CMakeFiles/spades-bwa.dir/bwtsw2_pair.c.o.d -o CMakeFiles/spades-bwa.dir/bwtsw2_pair.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwtsw2_pair.c [ 57%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/SourceMgr.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/SourceMgr.cpp.o -MF CMakeFiles/llvm-support.dir/SourceMgr.cpp.o.d -o CMakeFiles/llvm-support.dir/SourceMgr.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/SourceMgr.cpp [ 57%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringExtras.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/StringExtras.cpp.o -MF CMakeFiles/llvm-support.dir/StringExtras.cpp.o.d -o CMakeFiles/llvm-support.dir/StringExtras.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/StringExtras.cpp [ 57%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringMap.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/StringMap.cpp.o -MF CMakeFiles/llvm-support.dir/StringMap.cpp.o.d -o CMakeFiles/llvm-support.dir/StringMap.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/StringMap.cpp [ 58%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringRef.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/StringRef.cpp.o -MF CMakeFiles/llvm-support.dir/StringRef.cpp.o.d -o CMakeFiles/llvm-support.dir/StringRef.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/StringRef.cpp [ 59%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o -MF CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o.d -o CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/hmmdwrkr.c [ 59%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdutils.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdutils.c.o -MF CMakeFiles/hmmer.dir/src/hmmdutils.c.o.d -o CMakeFiles/hmmer.dir/src/hmmdutils.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/hmmdutils.c [ 59%] Linking C executable ../../bin/spades-bwa cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-bwa.dir/link.txt --verbose=1 [ 59%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmer.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/hmmer.c.o -MF CMakeFiles/hmmer.dir/src/hmmer.c.o.d -o CMakeFiles/hmmer.dir/src/hmmer.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/hmmer.c [ 59%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/logsum.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/logsum.c.o -MF CMakeFiles/hmmer.dir/src/logsum.c.o.d -o CMakeFiles/hmmer.dir/src/logsum.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/logsum.c [ 59%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/modelconfig.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/modelconfig.c.o -MF CMakeFiles/hmmer.dir/src/modelconfig.c.o.d -o CMakeFiles/hmmer.dir/src/modelconfig.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/modelconfig.c /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/spades-bwa.dir/link.d "CMakeFiles/spades-bwa.dir/main.c.o" "CMakeFiles/spades-bwa.dir/fastmap.c.o" "CMakeFiles/spades-bwa.dir/pemerge.c.o" "CMakeFiles/spades-bwa.dir/maxk.c.o" "CMakeFiles/spades-bwa.dir/kopen.c.o" "CMakeFiles/spades-bwa.dir/bwtaln.c.o" "CMakeFiles/spades-bwa.dir/bwtgap.c.o" "CMakeFiles/spades-bwa.dir/bwaseqio.c.o" "CMakeFiles/spades-bwa.dir/bamlite.c.o" "CMakeFiles/spades-bwa.dir/bwtsw2_main.c.o" "CMakeFiles/spades-bwa.dir/bwashm.c.o" "CMakeFiles/spades-bwa.dir/bwtsw2_aux.c.o" "CMakeFiles/spades-bwa.dir/bwtsw2_core.c.o" "CMakeFiles/spades-bwa.dir/bwtsw2_chain.c.o" "CMakeFiles/spades-bwa.dir/bwt_lite.c.o" "CMakeFiles/spades-bwa.dir/bwape.c.o" "CMakeFiles/spades-bwa.dir/bwase.c.o" "CMakeFiles/spades-bwa.dir/bwtsw2_pair.c.o" -o ../../bin/spades-bwa libbwa.a ../../_deps/zlib_ng-build/libz.a -lm make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 59%] Built target spades-bwa [ 59%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringSaver.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/StringSaver.cpp.o -MF CMakeFiles/llvm-support.dir/StringSaver.cpp.o.d -o CMakeFiles/llvm-support.dir/StringSaver.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/StringSaver.cpp [ 59%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o -MF CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o.d -o CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/ThreadLocal.cpp [ 59%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/modelstats.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/modelstats.c.o -MF CMakeFiles/hmmer.dir/src/modelstats.c.o.d -o CMakeFiles/hmmer.dir/src/modelstats.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/modelstats.c [ 60%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/mpisupport.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/mpisupport.c.o -MF CMakeFiles/hmmer.dir/src/mpisupport.c.o.d -o CMakeFiles/hmmer.dir/src/mpisupport.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/mpisupport.c [ 60%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Threading.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Threading.cpp.o -MF CMakeFiles/llvm-support.dir/Threading.cpp.o.d -o CMakeFiles/llvm-support.dir/Threading.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Threading.cpp [ 60%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/seqmodel.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/seqmodel.c.o -MF CMakeFiles/hmmer.dir/src/seqmodel.c.o.d -o CMakeFiles/hmmer.dir/src/seqmodel.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/seqmodel.c [ 60%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o -MF CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o.d -o CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/TimeProfiler.cpp [ 60%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/tracealign.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/tracealign.c.o -MF CMakeFiles/hmmer.dir/src/tracealign.c.o.d -o CMakeFiles/hmmer.dir/src/tracealign.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/tracealign.c [ 60%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o -MF CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o.d -o CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_alidisplay.c [ 60%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Twine.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Twine.cpp.o -MF CMakeFiles/llvm-support.dir/Twine.cpp.o.d -o CMakeFiles/llvm-support.dir/Twine.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Twine.cpp [ 60%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_bg.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_bg.c.o -MF CMakeFiles/hmmer.dir/src/p7_bg.c.o.d -o CMakeFiles/hmmer.dir/src/p7_bg.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_bg.c [ 60%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_builder.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer 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ext/hmmer/CMakeFiles/hmmer.dir/src/p7_builder.c.o -MF CMakeFiles/hmmer.dir/src/p7_builder.c.o.d -o CMakeFiles/hmmer.dir/src/p7_builder.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_builder.c [ 62%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Unicode.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Unicode.cpp.o -MF CMakeFiles/llvm-support.dir/Unicode.cpp.o.d -o CMakeFiles/llvm-support.dir/Unicode.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Unicode.cpp [ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_domaindef.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_domaindef.c.o -MF CMakeFiles/hmmer.dir/src/p7_domaindef.c.o.d -o CMakeFiles/hmmer.dir/src/p7_domaindef.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_domaindef.c [ 63%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/WithColor.cpp.o cd 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/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/WithColor.cpp [ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gmx.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gmx.c.o -MF CMakeFiles/hmmer.dir/src/p7_gmx.c.o.d -o CMakeFiles/hmmer.dir/src/p7_gmx.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_gmx.c [ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gbands.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gbands.c.o -MF CMakeFiles/hmmer.dir/src/p7_gbands.c.o.d -o CMakeFiles/hmmer.dir/src/p7_gbands.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_gbands.c [ 63%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/YAMLParser.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/YAMLParser.cpp.o -MF CMakeFiles/llvm-support.dir/YAMLParser.cpp.o.d -o CMakeFiles/llvm-support.dir/YAMLParser.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/YAMLParser.cpp [ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gmxb.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gmxb.c.o -MF CMakeFiles/hmmer.dir/src/p7_gmxb.c.o.d -o CMakeFiles/hmmer.dir/src/p7_gmxb.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_gmxb.c [ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gmxchk.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gmxchk.c.o -MF CMakeFiles/hmmer.dir/src/p7_gmxchk.c.o.d -o CMakeFiles/hmmer.dir/src/p7_gmxchk.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_gmxchk.c [ 63%] Linking CXX static library libgraphio.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/cmake -P CMakeFiles/graphio.dir/cmake_clean_target.cmake [ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmm.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmm.c.o -MF CMakeFiles/hmmer.dir/src/p7_hmm.c.o.d -o CMakeFiles/hmmer.dir/src/p7_hmm.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_hmm.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphio.dir/link.txt --verbose=1 [ 64%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmmcache.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmmcache.c.o -MF CMakeFiles/hmmer.dir/src/p7_hmmcache.c.o.d -o CMakeFiles/hmmer.dir/src/p7_hmmcache.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_hmmcache.c [ 64%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmmfile.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer 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ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmmfile.c.o -MF CMakeFiles/hmmer.dir/src/p7_hmmfile.c.o.d -o CMakeFiles/hmmer.dir/src/p7_hmmfile.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_hmmfile.c [ 64%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmmwindow.c.o [ 64%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o [ 64%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmmwindow.c.o -MF CMakeFiles/hmmer.dir/src/p7_hmmwindow.c.o.d -o CMakeFiles/hmmer.dir/src/p7_hmmwindow.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_hmmwindow.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o -MF CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o.d -o CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/YAMLTraits.cpp cd 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/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/raw_os_ostream.cpp [ 64%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_null3.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_null3.c.o -MF CMakeFiles/hmmer.dir/src/p7_null3.c.o.d -o CMakeFiles/hmmer.dir/src/p7_null3.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_null3.c [ 64%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_pipeline.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_pipeline.c.o -MF CMakeFiles/hmmer.dir/src/p7_pipeline.c.o.d -o CMakeFiles/hmmer.dir/src/p7_pipeline.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_pipeline.c /usr/bin/ar qc libgraphio.a CMakeFiles/graphio.dir/gfa.cpp.o CMakeFiles/graphio.dir/gfa_reader.cpp.o CMakeFiles/graphio.dir/gfa_writer.cpp.o CMakeFiles/graphio.dir/fastg_writer.cpp.o /usr/bin/ranlib libgraphio.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_prior.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_prior.c.o -MF CMakeFiles/hmmer.dir/src/p7_prior.c.o.d -o CMakeFiles/hmmer.dir/src/p7_prior.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_prior.c [ 65%] Built target graphio [ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_profile.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_profile.c.o -MF CMakeFiles/hmmer.dir/src/p7_profile.c.o.d -o CMakeFiles/hmmer.dir/src/p7_profile.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_profile.c [ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_spensemble.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_spensemble.c.o -MF CMakeFiles/hmmer.dir/src/p7_spensemble.c.o.d -o CMakeFiles/hmmer.dir/src/p7_spensemble.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_spensemble.c [ 67%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/raw_ostream.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/raw_ostream.cpp.o -MF CMakeFiles/llvm-support.dir/raw_ostream.cpp.o.d -o CMakeFiles/llvm-support.dir/raw_ostream.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/raw_ostream.cpp [ 67%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regcomp.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regcomp.c.o -MF CMakeFiles/llvm-support.dir/regcomp.c.o.d -o CMakeFiles/llvm-support.dir/regcomp.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/regcomp.c [ 67%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_tophits.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_tophits.c.o -MF CMakeFiles/hmmer.dir/src/p7_tophits.c.o.d -o CMakeFiles/hmmer.dir/src/p7_tophits.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_tophits.c [ 67%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_trace.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_trace.c.o -MF CMakeFiles/hmmer.dir/src/p7_trace.c.o.d -o CMakeFiles/hmmer.dir/src/p7_trace.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_trace.c [ 67%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_scoredata.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_scoredata.c.o -MF CMakeFiles/hmmer.dir/src/p7_scoredata.c.o.d -o CMakeFiles/hmmer.dir/src/p7_scoredata.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_scoredata.c [ 68%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hit.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hit.c.o -MF CMakeFiles/hmmer.dir/src/p7_hit.c.o.d -o CMakeFiles/hmmer.dir/src/p7_hit.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_hit.c [ 68%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_domain.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_domain.c.o -MF CMakeFiles/hmmer.dir/src/p7_domain.c.o.d -o CMakeFiles/hmmer.dir/src/p7_domain.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_domain.c [ 68%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regerror.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regerror.c.o -MF CMakeFiles/llvm-support.dir/regerror.c.o.d -o CMakeFiles/llvm-support.dir/regerror.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/regerror.c [ 68%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmpgmd2msa.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/hmmpgmd2msa.c.o -MF CMakeFiles/hmmer.dir/src/hmmpgmd2msa.c.o.d -o CMakeFiles/hmmer.dir/src/hmmpgmd2msa.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/hmmpgmd2msa.c [ 68%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/fm_alphabet.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/fm_alphabet.c.o -MF CMakeFiles/hmmer.dir/src/fm_alphabet.c.o.d -o CMakeFiles/hmmer.dir/src/fm_alphabet.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/fm_alphabet.c [ 68%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regexec.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regexec.c.o -MF CMakeFiles/llvm-support.dir/regexec.c.o.d -o CMakeFiles/llvm-support.dir/regexec.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/regexec.c [ 68%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/fm_general.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/fm_sse.c.o -MF CMakeFiles/hmmer.dir/src/fm_sse.c.o.d -o CMakeFiles/hmmer.dir/src/fm_sse.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/fm_sse.c [ 68%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/decoding.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/decoding.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/decoding.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/decoding.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/impl_sse/decoding.c [ 69%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/fm_ssv.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/fm_ssv.c.o -MF CMakeFiles/hmmer.dir/src/fm_ssv.c.o.d -o CMakeFiles/hmmer.dir/src/fm_ssv.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/fm_ssv.c [ 69%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regfree.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration 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-I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regstrlcpy.c.o -MF CMakeFiles/llvm-support.dir/regstrlcpy.c.o.d -o CMakeFiles/llvm-support.dir/regstrlcpy.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/regstrlcpy.c [ 69%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o [ 69%] Linking CXX static library libbinary_io.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer 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ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/impl_sse/fwdback.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/cmake -P CMakeFiles/binary_io.dir/cmake_clean_target.cmake [ 69%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/io.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common 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cmake_link_script CMakeFiles/binary_io.dir/link.txt --verbose=1 [ 69%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/impl_sse/ssvfilter.c [ 69%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer 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ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/impl_sse/msvfilter.c [ 70%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/impl_sse/null2.c [ 70%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/impl_sse/optacc.c /usr/bin/ar qc libbinary_io.a CMakeFiles/binary_io.dir/graph_pack.cpp.o CMakeFiles/binary_io.dir/genomic_info.cpp.o /usr/bin/ranlib libbinary_io.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 70%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o [ 70%] Built target binary_io make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/depend cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/impl_sse/stotrace.c make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/DependInfo.cmake "--color=" [ 70%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/impl_sse/vitfilter.c make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 70%] Building CXX object common/io/CMakeFiles/input.dir/reads/parser.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/parser.cpp.o -MF CMakeFiles/input.dir/reads/parser.cpp.o.d -o CMakeFiles/input.dir/reads/parser.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/reads/parser.cpp [ 70%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/impl_sse/p7_omx.c [ 71%] Building CXX object common/io/CMakeFiles/input.dir/reads/paired_readers.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/paired_readers.cpp.o -MF CMakeFiles/input.dir/reads/paired_readers.cpp.o.d -o CMakeFiles/input.dir/reads/paired_readers.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/reads/paired_readers.cpp [ 71%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/impl_sse/p7_oprofile.c [ 71%] Building CXX object common/io/CMakeFiles/input.dir/reads/binary_converter.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/binary_converter.cpp.o -MF CMakeFiles/input.dir/reads/binary_converter.cpp.o.d -o CMakeFiles/input.dir/reads/binary_converter.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/reads/binary_converter.cpp [ 73%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/impl_sse/mpi.c [ 73%] Building CXX object common/io/CMakeFiles/input.dir/reads/binary_streams.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/binary_streams.cpp.o -MF CMakeFiles/input.dir/reads/binary_streams.cpp.o.d -o CMakeFiles/input.dir/reads/binary_streams.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/reads/binary_streams.cpp [ 73%] Building CXX object common/io/CMakeFiles/input.dir/reads/io_helper.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/io_helper.cpp.o -MF CMakeFiles/input.dir/reads/io_helper.cpp.o.d -o CMakeFiles/input.dir/reads/io_helper.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/reads/io_helper.cpp make -f common/toolchain/CMakeFiles/toolchain.dir/build.make common/toolchain/CMakeFiles/toolchain.dir/depend [ 73%] Building CXX object common/io/CMakeFiles/input.dir/dataset_support/read_converter.cpp.o make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/toolchain /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/toolchain /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/toolchain/CMakeFiles/toolchain.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/dataset_support/read_converter.cpp.o -MF CMakeFiles/input.dir/dataset_support/read_converter.cpp.o.d -o CMakeFiles/input.dir/dataset_support/read_converter.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/dataset_support/read_converter.cpp make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/toolchain/CMakeFiles/toolchain.dir/build.make common/toolchain/CMakeFiles/toolchain.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 73%] Building CXX object common/toolchain/CMakeFiles/toolchain.dir/utils.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/toolchain && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/toolchain/CMakeFiles/toolchain.dir/utils.cpp.o -MF CMakeFiles/toolchain.dir/utils.cpp.o.d -o CMakeFiles/toolchain.dir/utils.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/toolchain/utils.cpp [ 73%] Building CXX object common/io/CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o -MF CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o.d -o CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/dataset_support/dataset_readers.cpp [ 74%] Linking CXX static library libllvm-support.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cmake -P CMakeFiles/llvm-support.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cmake -E cmake_link_script CMakeFiles/llvm-support.dir/link.txt --verbose=1 /usr/bin/ar qc libllvm-support.a "CMakeFiles/llvm-support.dir/APFloat.cpp.o" "CMakeFiles/llvm-support.dir/APInt.cpp.o" "CMakeFiles/llvm-support.dir/Atomic.cpp.o" "CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o" "CMakeFiles/llvm-support.dir/Debug.cpp.o" "CMakeFiles/llvm-support.dir/Errno.cpp.o" "CMakeFiles/llvm-support.dir/Error.cpp.o" "CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o" "CMakeFiles/llvm-support.dir/FoldingSet.cpp.o" "CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o" "CMakeFiles/llvm-support.dir/Hashing.cpp.o" "CMakeFiles/llvm-support.dir/Host.cpp.o" "CMakeFiles/llvm-support.dir/JSON.cpp.o" "CMakeFiles/llvm-support.dir/LEB128.cpp.o" "CMakeFiles/llvm-support.dir/LineIterator.cpp.o" "CMakeFiles/llvm-support.dir/Locale.cpp.o" "CMakeFiles/llvm-support.dir/MD5.cpp.o" "CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o" "CMakeFiles/llvm-support.dir/MemAlloc.cpp.o" "CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o" "CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o" "CMakeFiles/llvm-support.dir/Path.cpp.o" "CMakeFiles/llvm-support.dir/Process.cpp.o" "CMakeFiles/llvm-support.dir/Program.cpp.o" "CMakeFiles/llvm-support.dir/Regex.cpp.o" "CMakeFiles/llvm-support.dir/Signals.cpp.o" "CMakeFiles/llvm-support.dir/SmallVector.cpp.o" "CMakeFiles/llvm-support.dir/SourceMgr.cpp.o" "CMakeFiles/llvm-support.dir/StringExtras.cpp.o" "CMakeFiles/llvm-support.dir/StringMap.cpp.o" "CMakeFiles/llvm-support.dir/StringRef.cpp.o" "CMakeFiles/llvm-support.dir/StringSaver.cpp.o" "CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o" "CMakeFiles/llvm-support.dir/Threading.cpp.o" "CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o" "CMakeFiles/llvm-support.dir/Twine.cpp.o" "CMakeFiles/llvm-support.dir/Unicode.cpp.o" "CMakeFiles/llvm-support.dir/WithColor.cpp.o" "CMakeFiles/llvm-support.dir/YAMLParser.cpp.o" "CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o" "CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o" "CMakeFiles/llvm-support.dir/raw_ostream.cpp.o" "CMakeFiles/llvm-support.dir/regcomp.c.o" "CMakeFiles/llvm-support.dir/regerror.c.o" "CMakeFiles/llvm-support.dir/regexec.c.o" "CMakeFiles/llvm-support.dir/regfree.c.o" "CMakeFiles/llvm-support.dir/regstrlcpy.c.o" /usr/bin/ranlib libllvm-support.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 74%] Built target llvm-support make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 74%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o -MF CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o.d -o CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/id_distributor.cpp [ 74%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o -MF CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o.d -o CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/components/connected_component.cpp [ 75%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o -MF CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o.d -o CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/paths/bidirectional_path.cpp [ 75%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o -MF CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o.d -o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/toolchain/utils.cpp:10: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/toolchain/utils.cpp:62:63: required from here 62 | io::binary::BasicGraphIO().Load(filename, graph); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:31:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 31 | bool loaded = Base::Load(basename, graph); | ^~~~~~ [ 75%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o -MF CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o.d -o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:43:10: required from here 43 | bool BinRead(std::istream &is, Graph &graph) override { | ^~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:44:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 44 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:10: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:47:10: required from here 47 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:61:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 61 | auto new_id = graph.AddVertex(typename Graph::VertexData(graph.k()), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:83:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 83 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ [ 75%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o -MF CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o.d -o CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/coverage_uniformity_analyzer.cpp [ 75%] Linking C static library libhmmer.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cmake -P CMakeFiles/hmmer.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cmake -E cmake_link_script CMakeFiles/hmmer.dir/link.txt --verbose=1 /usr/bin/ar qc libhmmer.a CMakeFiles/hmmer.dir/src/build.c.o CMakeFiles/hmmer.dir/src/cachedb.c.o CMakeFiles/hmmer.dir/src/emit.c.o CMakeFiles/hmmer.dir/src/errors.c.o CMakeFiles/hmmer.dir/src/evalues.c.o CMakeFiles/hmmer.dir/src/eweight.c.o CMakeFiles/hmmer.dir/src/generic_decoding.c.o CMakeFiles/hmmer.dir/src/generic_fwdback.c.o CMakeFiles/hmmer.dir/src/generic_fwdback_chk.c.o CMakeFiles/hmmer.dir/src/generic_fwdback_banded.c.o CMakeFiles/hmmer.dir/src/generic_null2.c.o CMakeFiles/hmmer.dir/src/generic_msv.c.o CMakeFiles/hmmer.dir/src/generic_optacc.c.o CMakeFiles/hmmer.dir/src/generic_stotrace.c.o CMakeFiles/hmmer.dir/src/generic_viterbi.c.o CMakeFiles/hmmer.dir/src/generic_vtrace.c.o CMakeFiles/hmmer.dir/src/h2_io.c.o CMakeFiles/hmmer.dir/src/heatmap.c.o CMakeFiles/hmmer.dir/src/hmmlogo.c.o CMakeFiles/hmmer.dir/src/hmmdmstr.c.o CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o CMakeFiles/hmmer.dir/src/hmmdutils.c.o CMakeFiles/hmmer.dir/src/hmmer.c.o CMakeFiles/hmmer.dir/src/logsum.c.o CMakeFiles/hmmer.dir/src/modelconfig.c.o CMakeFiles/hmmer.dir/src/modelstats.c.o CMakeFiles/hmmer.dir/src/mpisupport.c.o CMakeFiles/hmmer.dir/src/seqmodel.c.o CMakeFiles/hmmer.dir/src/tracealign.c.o CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o CMakeFiles/hmmer.dir/src/p7_bg.c.o CMakeFiles/hmmer.dir/src/p7_builder.c.o CMakeFiles/hmmer.dir/src/p7_domaindef.c.o CMakeFiles/hmmer.dir/src/p7_gbands.c.o CMakeFiles/hmmer.dir/src/p7_gmx.c.o CMakeFiles/hmmer.dir/src/p7_gmxb.c.o CMakeFiles/hmmer.dir/src/p7_gmxchk.c.o CMakeFiles/hmmer.dir/src/p7_hmm.c.o CMakeFiles/hmmer.dir/src/p7_hmmcache.c.o CMakeFiles/hmmer.dir/src/p7_hmmfile.c.o CMakeFiles/hmmer.dir/src/p7_hmmwindow.c.o CMakeFiles/hmmer.dir/src/p7_null3.c.o CMakeFiles/hmmer.dir/src/p7_pipeline.c.o CMakeFiles/hmmer.dir/src/p7_prior.c.o CMakeFiles/hmmer.dir/src/p7_profile.c.o CMakeFiles/hmmer.dir/src/p7_spensemble.c.o CMakeFiles/hmmer.dir/src/p7_tophits.c.o CMakeFiles/hmmer.dir/src/p7_trace.c.o CMakeFiles/hmmer.dir/src/p7_scoredata.c.o CMakeFiles/hmmer.dir/src/p7_hit.c.o CMakeFiles/hmmer.dir/src/p7_domain.c.o CMakeFiles/hmmer.dir/src/hmmpgmd2msa.c.o CMakeFiles/hmmer.dir/src/fm_alphabet.c.o CMakeFiles/hmmer.dir/src/fm_general.c.o CMakeFiles/hmmer.dir/src/fm_sse.c.o CMakeFiles/hmmer.dir/src/fm_ssv.c.o CMakeFiles/hmmer.dir/src/impl_sse/decoding.c.o CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o CMakeFiles/hmmer.dir/src/impl_sse/io.c.o CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o /usr/bin/ranlib libhmmer.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 75%] Built target hmmer make -f common/hmm/CMakeFiles/hmmercpp.dir/build.make common/hmm/CMakeFiles/hmmercpp.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/hmm /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/hmm /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/hmm/CMakeFiles/hmmercpp.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/hmm/CMakeFiles/hmmercpp.dir/build.make common/hmm/CMakeFiles/hmmercpp.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 75%] Building CXX object common/hmm/CMakeFiles/hmmercpp.dir/hmmfile.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/hmm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/hmm/CMakeFiles/hmmercpp.dir/hmmfile.cpp.o -MF CMakeFiles/hmmercpp.dir/hmmfile.cpp.o.d -o CMakeFiles/hmmercpp.dir/hmmfile.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/hmm/hmmfile.cpp [ 75%] Building CXX object common/hmm/CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/hmm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/hmm/CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o -MF CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o.d -o CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/hmm/hmmmatcher.cpp [ 75%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/__/alignment/edge_index_refiller.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/__/alignment/edge_index_refiller.cpp.o -MF CMakeFiles/assembly_graph.dir/__/alignment/edge_index_refiller.cpp.o.d -o CMakeFiles/assembly_graph.dir/__/alignment/edge_index_refiller.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/edge_index_refiller.cpp /build/reproducible-path/spades-4.0.0+dfsg1/src/common/hmm/hmmfile.cpp: In constructor 'hmmer::HMMFile::HMMFile(const std::string&)': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/hmm/hmmfile.cpp:53:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 53 | p7_Fail("File existence/permissions problem in trying to open HMM file %s.\n%s\n", hmmfile.c_str(), errbuf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/hmm/hmmfile.cpp:55:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 55 | p7_Fail("File format problem in trying to open HMM file %s.\n%s\n", hmmfile.c_str(), errbuf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/hmm/hmmfile.cpp:57:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 57 | p7_Fail("Unexpected error %d in opening HMM file %s.\n%s\n", status, hmmfile.c_str(), errbuf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/hmm/hmmmatcher.cpp: In member function 'P7_PIPELINE* hmmer::HMMMatcher::pipeline_create(const hmmer::hmmer_cfg&, int, int, int, unsigned int)': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/hmm/hmmmatcher.cpp:166:34: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 166 | pli->Z = pli->domZ = cfg.Z; | ~~~~^ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/paths/bidirectional_path.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:8: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp: In member function 'size_t debruijn_graph::DeBruijnGraph::link_length(VertexId, EdgeId, EdgeId) const': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp:142:5: warning: control reaches end of non-void function [-Wreturn-type] 142 | } | ^ [ 75%] Linking CXX static library libhmmercpp.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/hmm && /usr/bin/cmake -P CMakeFiles/hmmercpp.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/hmm && /usr/bin/cmake -E cmake_link_script CMakeFiles/hmmercpp.dir/link.txt --verbose=1 /usr/bin/ar qc libhmmercpp.a CMakeFiles/hmmercpp.dir/hmmfile.cpp.o CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o /usr/bin/ranlib libhmmercpp.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 75%] Built target hmmercpp make -f projects/spades/CMakeFiles/spades-stages.dir/build.make projects/spades/CMakeFiles/spades-stages.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades/CMakeFiles/spades-stages.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f projects/spades/CMakeFiles/spades-stages.dir/build.make projects/spades/CMakeFiles/spades-stages.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 75%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/pair_info_count.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/pair_info_count.cpp.o -MF CMakeFiles/spades-stages.dir/pair_info_count.cpp.o.d -o CMakeFiles/spades-stages.dir/pair_info_count.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/pair_info_count.cpp [ 75%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o -MF CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o.d -o CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/mismatch_correction.cpp [ 75%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/gap_closer.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/gap_closer.cpp.o -MF CMakeFiles/spades-stages.dir/gap_closer.cpp.o.d -o CMakeFiles/spades-stages.dir/gap_closer.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/gap_closer.cpp [ 76%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o -MF CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o.d -o CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/second_phase_setup.cpp [ 76%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/distance_estimation.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/distance_estimation.cpp.o -MF CMakeFiles/spades-stages.dir/distance_estimation.cpp.o.d -o CMakeFiles/spades-stages.dir/distance_estimation.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/distance_estimation.cpp [ 76%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o -MF CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o.d -o CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/repeat_resolving.cpp [ 76%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o -MF CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o.d -o CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/contig_output_stage.cpp [ 76%] Linking CXX static library libtoolchain.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/toolchain && /usr/bin/cmake -P CMakeFiles/toolchain.dir/cmake_clean_target.cmake /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/second_phase_setup.cpp: In member function 'virtual void debruijn_graph::SecondPhaseSetup::run(graph_pack::GraphPack&, const char*)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/second_phase_setup.cpp:26:9: warning: unused variable 'code' [-Wunused-variable] 26 | int code = rename(old_pe_contigs_filename.c_str(), new_pe_contigs_filename.c_str()); | ^~~~ cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/toolchain && /usr/bin/cmake -E cmake_link_script CMakeFiles/toolchain.dir/link.txt --verbose=1 In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/index/edge_info_updater.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/index/edge_index_builders.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/edge_index_refiller.cpp:10: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/index/edge_position_index.hpp: In instantiation of 'class debruijn_graph::EdgeInfo': /usr/include/c++/14/bits/stl_vector.h:1018:43: required from 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = debruijn_graph::EdgeInfo; _Alloc = std::allocator >; size_type = long unsigned int]' 1018 | _M_erase_at_end(this->_M_impl._M_start + __new_size); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/ph_map/perfect_hash_map.hpp:166:21: required from 'void kmers::PerfectHashMap::resize(size_t) [with K = RuntimeSeq<128>; V = debruijn_graph::EdgeInfo; traits = kmers::kmer_index_traits >; StoringType = kmers::InvertableStoring; Container = std::vector, std::allocator > >; size_t = long unsigned int]' 166 | data_.resize(sz); | ~~~~~~~~~~~~^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/ph_map/perfect_hash_map_builder.hpp:31:21: required from 'kmers::KMerDiskStorage kmers::PerfectHashMapBuilder::BuildIndex(kmers::PerfectHashMap&, Counter&, size_t, size_t, bool) const [with K = RuntimeSeq<128>; V = debruijn_graph::EdgeInfo; traits = kmers::kmer_index_traits >; StoringType = kmers::InvertableStoring; Counter = kmers::KMerDiskCounter >; typename Counter::Seq = RuntimeSeq<128>; size_t = long unsigned int]' 31 | index.resize(res.total_kmers()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/ph_map/perfect_hash_map_builder.hpp:140:39: required from 'void kmers::BuildIndex(PerfectHashMap&, Counter&, size_t, size_t, bool) [with K = RuntimeSeq<128>; V = debruijn_graph::EdgeInfo; traits = kmer_index_traits >; StoringType = InvertableStoring; Counter = KMerDiskCounter >; size_t = long unsigned int]' 140 | PerfectHashMapBuilder().BuildIndex(index, counter, bucket_num, thread_num, save_final); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/index/edge_index_builders.hpp:280:19: required from 'void debruijn_graph::GraphPositionFillingIndexBuilder::BuildIndexFromGraph(Index&, const debruijn_graph::Graph&, fs::impl::TmpDir, size_t) const [with Index = debruijn_graph::KmerFreeEdgeIndex; debruijn_graph::Graph = debruijn_graph::DeBruijnGraph; fs::impl::TmpDir = llvm::IntrusiveRefCntPtr; size_t = long unsigned int]' 280 | BuildIndex(index, counter, 10 * nthreads, nthreads); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/edge_index_refiller.cpp:29:43: required from 'void debruijn_graph::EdgeIndexRefiller::Refill(EdgeIndex&, const debruijn_graph::Graph&, bool) [with EdgeIndex = debruijn_graph::KmerFreeEdgeIndex; debruijn_graph::Graph = debruijn_graph::DeBruijnGraph]' 29 | IndexBuilder().BuildIndexFromGraph(index, g, fs::tmp::make_temp_dir(workdir_, "edge_index")); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/edge_index_refiller.cpp:36:70: required from here 36 | void EdgeIndexRefiller::Refill(EdgeIndex &index, const Graph &g, bool); | ^ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/index/edge_position_index.hpp:21:14: warning: ignoring packed attribute because of unpacked non-POD field 'omnigraph::impl::EdgeId debruijn_graph::EdgeInfo::edge_id_' 21 | IdHolder edge_id_; | ^~~~~~~~ /usr/bin/ar qc libtoolchain.a CMakeFiles/toolchain.dir/utils.cpp.o /usr/bin/ranlib libtoolchain.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 78%] Linking CXX static library libinput.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io && /usr/bin/cmake -P CMakeFiles/input.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io && /usr/bin/cmake -E cmake_link_script CMakeFiles/input.dir/link.txt --verbose=1 [ 78%] Built target toolchain [ 78%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o -MF CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o.d -o CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_aligning.cpp /usr/bin/ar qc libinput.a CMakeFiles/input.dir/reads/parser.cpp.o CMakeFiles/input.dir/reads/paired_readers.cpp.o CMakeFiles/input.dir/reads/binary_converter.cpp.o CMakeFiles/input.dir/reads/binary_streams.cpp.o CMakeFiles/input.dir/reads/io_helper.cpp.o CMakeFiles/input.dir/dataset_support/read_converter.cpp.o CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o /usr/bin/ranlib libinput.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 78%] Built target input make -f common/library/CMakeFiles/library.dir/build.make common/library/CMakeFiles/library.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/library /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/library /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/library/CMakeFiles/library.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/library/CMakeFiles/library.dir/build.make common/library/CMakeFiles/library.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 78%] Building CXX object common/library/CMakeFiles/library.dir/library.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/library && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/library/CMakeFiles/library.dir/library.cpp.o -MF CMakeFiles/library.dir/library.cpp.o.d -o CMakeFiles/library.dir/library.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/library/library.cpp [ 78%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o -MF CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o.d -o CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/chromosome_removal.cpp [ 79%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/extract_domains.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/extract_domains.cpp.o -MF CMakeFiles/spades-stages.dir/extract_domains.cpp.o.d -o CMakeFiles/spades-stages.dir/extract_domains.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/extract_domains.cpp [ 79%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/domain_matcher.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/domain_matcher.cpp.o -MF CMakeFiles/spades-stages.dir/domain_matcher.cpp.o.d -o CMakeFiles/spades-stages.dir/domain_matcher.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/domain_matcher.cpp In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/observable_graph.hpp:13, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/sequence_mapper_notifier.hpp:14, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/gap_closer.cpp:11: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 508 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/parallel_processing.hpp:378:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity; size_t = long unsigned int]' 378 | for (; !it_.IsEnd(); ++it_) { | ^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/compressor.hpp:130:26: required from 'size_t omnigraph::CompressAllVertices(Graph&, size_t, bool) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 130 | return compressor.Run(); | ~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/gap_closer.cpp:434:46: required from here 434 | omnigraph::CompressAllVertices(g_); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_aligning.cpp:11: /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp: In function 'std::string debruijn_graph::gap_closing::SPOAConsensus(const std::vector >&, const debruijn_graph::config::pacbio_processor&)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp:329:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 329 | while (pref_remove < coverages.size() && coverages[pref_remove] < cov / 2 ) | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp: In member function 'void debruijn_graph::gap_closing::MultiGapJoiner::UpdateGap(debruijn_graph::gap_closing::GapDescription&, debruijn_graph::gap_closing::EdgePair, debruijn_graph::gap_closing::EdgePair) const': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp:485:14: warning: unused variable 'u1' [-Wunused-variable] 485 | bool u1 = UpdateLeft(gap, split_orig, split_res); | ^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp:486:14: warning: unused variable 'u2' [-Wunused-variable] 486 | bool u2 = UpdateRight(gap, split_orig, split_res); | ^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp: In member function 'debruijn_graph::gap_closing::GapDescription debruijn_graph::gap_closing::HybridGapCloser::ConstructConsensus(gap_info_it, gap_info_it) const': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp:659:16: warning: unused variable 'cur_len' [-Wunused-variable] 659 | size_t cur_len = end_it - start_it; | ^~~~~~~ [ 79%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o -MF CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o.d -o CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/domain_graph_construction.cpp In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/stats/picture_dump.hpp:18, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/gap_closer.cpp:12: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:30:10: required from here 30 | bool Load(const std::string &basename, Graph &graph) override { | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:31:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 31 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:43:10: required from here 43 | bool BinRead(std::istream &is, Graph &graph) override { | ^~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:44:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 44 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:10: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:47:10: required from here 47 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:61:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 61 | auto new_id = graph.AddVertex(typename Graph::VertexData(graph.k()), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:83:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 83 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/domain_matcher.cpp: In function 'void nrps::MatchContigsInternal(hmmer::HMMMatcher&, const path_extend::BidirectionalPath&, const std::string&, const std::string&, const std::string&, ContigAlnInfo&, io::OFastaReadStream&, size_t, bool)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/domain_matcher.cpp:53:48: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 53 | if (seqpos2.second - seqpos2.first < model_length / 10) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ [ 79%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o -MF CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o.d -o CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/restricted_edges_filling.cpp In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/stats/picture_dump.hpp:18, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/repeat_resolving.cpp:11: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:30:10: required from here 30 | bool Load(const std::string &basename, Graph &graph) override { | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:31:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 31 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:43:10: required from here 43 | bool BinRead(std::istream &is, Graph &graph) override { | ^~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:44:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 44 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:10: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:47:10: required from here 47 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:61:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 61 | auto new_id = graph.AddVertex(typename Graph::VertexData(graph.k()), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:83:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 83 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/observable_graph.hpp:13, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_aligning.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_aligning.cpp:9: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 508 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/parallel_processing.hpp:378:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity; size_t = long unsigned int]' 378 | for (; !it_.IsEnd(); ++it_) { | ^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/compressor.hpp:130:26: required from 'size_t omnigraph::CompressAllVertices(Graph&, size_t, bool) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 130 | return compressor.Run(); | ~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp:752:28: required from here 752 | CompressAllVertices(g_, /*chunk_cnt*/100); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ [ 79%] Building CXX object common/library/CMakeFiles/library.dir/library_data.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/library && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/library/CMakeFiles/library.dir/library_data.cpp.o -MF CMakeFiles/library.dir/library_data.cpp.o.d -o CMakeFiles/library.dir/library_data.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/library/library_data.cpp /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/domain_graph_construction.cpp: In member function 'std::pair debruijn_graph::DomainGraphConstructor::FindMappingToPath(const path_extend::BidirectionalPath&, const omnigraph::MappingPath&, std::vector >&) const': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/domain_graph_construction.cpp:232:21: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 232 | for (;index != res.first; ++index) { | ~~~~~~^~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/domain_graph_construction.cpp: In member function 'void debruijn_graph::DomainGraphConstructor::ConstructStrongEdgesInternal(debruijn_graph::VertexId, const path_extend::BidirectionalPath&, std::map, std::vector > > >, PairComparator> >&)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/domain_graph_construction.cpp:259:34: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 259 | if (coords.second + 5000 > path.Length()) { | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/stats/picture_dump.hpp:18, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_aligning.cpp:17: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:30:10: required from here 30 | bool Load(const std::string &basename, Graph &graph) override { | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:31:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 31 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:43:10: required from here 43 | bool BinRead(std::istream &is, Graph &graph) override { | ^~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:44:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 44 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:10: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:47:10: required from here 47 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:61:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 61 | auto new_id = graph.AddVertex(typename Graph::VertexData(graph.k()), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:83:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 83 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ [ 79%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/load_graph.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/load_graph.cpp.o -MF CMakeFiles/spades-stages.dir/load_graph.cpp.o.d -o CMakeFiles/spades-stages.dir/load_graph.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/load_graph.cpp [ 79%] Linking CXX static library liblibrary.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/library && /usr/bin/cmake -P CMakeFiles/library.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/library && /usr/bin/cmake -E cmake_link_script CMakeFiles/library.dir/link.txt --verbose=1 /usr/bin/ar qc liblibrary.a CMakeFiles/library.dir/library.cpp.o CMakeFiles/library.dir/library_data.cpp.o /usr/bin/ranlib liblibrary.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 79%] Built target library make -f common/configs/CMakeFiles/configs.dir/build.make common/configs/CMakeFiles/configs.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/configs /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/configs /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/configs/CMakeFiles/configs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/configs/CMakeFiles/configs.dir/build.make common/configs/CMakeFiles/configs.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 79%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/domain_graph.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/domain_graph.cpp.o -MF CMakeFiles/spades-stages.dir/domain_graph.cpp.o.d -o CMakeFiles/spades-stages.dir/domain_graph.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/domain_graph.cpp [ 79%] Building CXX object common/configs/CMakeFiles/configs.dir/config_struct.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/configs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/configs/CMakeFiles/configs.dir/config_struct.cpp.o -MF CMakeFiles/configs.dir/config_struct.cpp.o.d -o CMakeFiles/configs.dir/config_struct.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/configs/config_struct.cpp [ 80%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/wastewater_disentangle.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/wastewater_disentangle.cpp.o -MF CMakeFiles/spades-stages.dir/wastewater_disentangle.cpp.o.d -o CMakeFiles/spades-stages.dir/wastewater_disentangle.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/wastewater_disentangle.cpp [ 81%] Building CXX object common/configs/CMakeFiles/configs.dir/pe_config_struct.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/configs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/configs/CMakeFiles/configs.dir/pe_config_struct.cpp.o -MF CMakeFiles/configs.dir/pe_config_struct.cpp.o.d -o CMakeFiles/configs.dir/pe_config_struct.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/configs/pe_config_struct.cpp [ 81%] Linking CXX static library libassembly_graph.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/cmake -P CMakeFiles/assembly_graph.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/cmake -E cmake_link_script CMakeFiles/assembly_graph.dir/link.txt --verbose=1 /usr/bin/ar qc libassembly_graph.a CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o CMakeFiles/assembly_graph.dir/__/alignment/edge_index_refiller.cpp.o /usr/bin/ranlib libassembly_graph.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 81%] Built target assembly_graph make -f common/alignment/CMakeFiles/alignment.dir/build.make common/alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment/CMakeFiles/alignment.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/alignment/CMakeFiles/alignment.dir/build.make common/alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 81%] Building CXX object common/alignment/CMakeFiles/alignment.dir/long_read_mapper.cpp.o [ 81%] Building CXX object common/alignment/CMakeFiles/alignment.dir/gap_info.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/alignment/CMakeFiles/alignment.dir/gap_info.cpp.o -MF CMakeFiles/alignment.dir/gap_info.cpp.o.d -o CMakeFiles/alignment.dir/gap_info.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/gap_info.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/alignment/CMakeFiles/alignment.dir/long_read_mapper.cpp.o -MF CMakeFiles/alignment.dir/long_read_mapper.cpp.o.d -o CMakeFiles/alignment.dir/long_read_mapper.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/long_read_mapper.cpp [ 81%] Building CXX object common/alignment/CMakeFiles/alignment.dir/sequence_mapper_notifier.cpp.o [ 81%] Building CXX object common/alignment/CMakeFiles/alignment.dir/bwa_index.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/alignment/CMakeFiles/alignment.dir/bwa_index.cpp.o -MF CMakeFiles/alignment.dir/bwa_index.cpp.o.d -o CMakeFiles/alignment.dir/bwa_index.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/bwa_index.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/alignment/CMakeFiles/alignment.dir/sequence_mapper_notifier.cpp.o -MF CMakeFiles/alignment.dir/sequence_mapper_notifier.cpp.o.d -o CMakeFiles/alignment.dir/sequence_mapper_notifier.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/sequence_mapper_notifier.cpp [ 81%] Building CXX object common/alignment/CMakeFiles/alignment.dir/kmer_sequence_mapper.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/alignment/CMakeFiles/alignment.dir/kmer_sequence_mapper.cpp.o -MF CMakeFiles/alignment.dir/kmer_sequence_mapper.cpp.o.d -o CMakeFiles/alignment.dir/kmer_sequence_mapper.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/kmer_sequence_mapper.cpp In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/bwa_index.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/bwa_index.cpp:8: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/bwa_index.cpp: In member function 'omnigraph::MappingPath alignment::BWAIndex::GetMappingPath(const mem_alnreg_v&, const Sequence&, bool) const': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/bwa_index.cpp:335:29: warning: format '%lld' expects argument of type 'long long int', but argument 5 has type 'long unsigned int' [-Wformat=] 335 | fprintf(stderr, "%zu: [%zu, %lld)\t[%d, %d) %c %ld %s %d %d\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 336 | i, 337 | pos, pos + a.re - a.rb, a.qb, a.qe, | ~~~~~~~~~~~~~~~~~ | | | long unsigned int /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/logger/logger.hpp:152:13: note: in definition of macro 'LOG_EXPR' 152 | expr; \ | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/bwa_index.cpp:331:9: note: in expansion of macro 'DEBUG_EXPR' 331 | DEBUG_EXPR({ | ^~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/bwa_index.cpp:335:44: note: format string is defined here 335 | fprintf(stderr, "%zu: [%zu, %lld)\t[%d, %d) %c %ld %s %d %d\n", | ~~~^ | | | long long int | %ld [ 82%] Building CXX object common/alignment/CMakeFiles/alignment.dir/pacbio/gap_filler.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/alignment/CMakeFiles/alignment.dir/pacbio/gap_filler.cpp.o -MF CMakeFiles/alignment.dir/pacbio/gap_filler.cpp.o.d -o CMakeFiles/alignment.dir/pacbio/gap_filler.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/pacbio/gap_filler.cpp [ 82%] Building CXX object common/alignment/CMakeFiles/alignment.dir/pacbio/gap_dijkstra.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/alignment/CMakeFiles/alignment.dir/pacbio/gap_dijkstra.cpp.o -MF CMakeFiles/alignment.dir/pacbio/gap_dijkstra.cpp.o.d -o CMakeFiles/alignment.dir/pacbio/gap_dijkstra.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/pacbio/gap_dijkstra.cpp /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/long_read_mapper.cpp: In member function 'void debruijn_graph::{anonymous}::GappedPathExtractorForTrustedContigs::RemoveMappingsWithBadTotalLength(omnigraph::MappingPath&) const': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/long_read_mapper.cpp:280:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 280 | if (bad_mapping_pos == -1) | ~~~~~~~~~~~~~~~~^~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/bits/alloc_traits.h:39, from /usr/include/c++/14/ext/alloc_traits.h:34, from /usr/include/c++/14/bits/hashtable_policy.h:39, from /usr/include/c++/14/bits/hashtable.h:35, from /usr/include/c++/14/bits/unordered_map.h:33, from /usr/include/c++/14/unordered_map:41, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/pack.hpp:14, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline/graph_pack.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline/stage.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/gap_closer.hpp:18, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/gap_closer.cpp:9: In member function 'void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = phmap::priv::Deallocate<8, std::allocator > > > > >(std::allocator > > > >*, void*, size_t)::M]', inlined from 'static void phmap::allocator_traits::deallocate(Alloc&, pointer, size_type) [with Alloc = std::allocator > > > > >(std::allocator > > > >*, void*, size_t)::M>]' at /usr/include/parallel_hashmap/phmap_base.h:1487:21, inlined from 'void phmap::priv::Deallocate(Alloc*, void*, size_t) [with long unsigned int Alignment = 8; Alloc = std::allocator > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:4210:17, inlined from 'void phmap::priv::btree::deallocate(size_type, node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2003:60, inlined from 'void phmap::priv::btree::delete_leaf_node(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2013:23, inlined from 'void phmap::priv::btree::internal_clear(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:3228:29, inlined from 'void phmap::priv::btree::clear() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2859:27, inlined from 'phmap::priv::btree::~btree() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:1704:18, inlined from 'phmap::priv::btree_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_container()' at /usr/include/parallel_hashmap/btree.h:3264:11, inlined from 'phmap::priv::btree_set_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_set_container()' at /usr/include/parallel_hashmap/btree.h:3429:11, inlined from 'phmap::priv::btree_map_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_map_container()' at /usr/include/parallel_hashmap/btree.h:3591:11, inlined from 'phmap::btree_map > >, phmap::Less, std::allocator > > > > >::~btree_map()' at /usr/include/parallel_hashmap/btree.h:3952:15, inlined from 'omnigraph::de::NoLockingConstAdapter > >, phmap::Less, std::allocator > > > > > >::~NoLockingConstAdapter()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info.hpp:567:7, inlined from 'std::pair > >, phmap::Less, std::allocator > > > > > > >::~pair()' at /usr/include/c++/14/bits/stl_pair.h:284:12, inlined from 'void std::__new_allocator<_Tp>::destroy(_Up*) [with _Up = std::pair > >, phmap::Less, std::allocator > > > > > > >; _Tp = std::pair > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/c++/14/bits/new_allocator.h:198:13, inlined from 'static void std::allocator_traits >::destroy(allocator_type&, _Up*) [with _Up = std::pair > >, phmap::Less, std::allocator > > > > > > >; _Tp = std::pair > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/c++/14/bits/alloc_traits.h:597:15, inlined from 'static decltype (std::allocator_traits::destroy(a, p)) phmap::allocator_traits::destroy_impl(int, A&, T*) [with A = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; T = std::pair > >, phmap::Less, std::allocator > > > > > > >; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:1546:42, inlined from 'static void phmap::allocator_traits::destroy(Alloc&, T*) [with T = std::pair > >, phmap::Less, std::allocator > > > > > > >; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:1504:21, inlined from 'static void phmap::priv::map_slot_policy::swap(Allocator*, slot_type*, slot_type*) [with Allocator = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; K = omnigraph::impl::EdgeId; V = omnigraph::de::NoLockingConstAdapter > >, phmap::Less, std::allocator > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:4554:56, inlined from 'static void phmap::priv::common_params::swap(Alloc*, slot_type*, slot_type*) [with Key = omnigraph::impl::EdgeId; Compare = phmap::Less; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; int TargetNodeSize = 256; bool Multi = false; SlotPolicy = phmap::priv::map_slot_policy > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/parallel_hashmap/btree.h:888:30, inlined from 'void phmap::priv::btree_node::swap(phmap::priv::btree_node*, allocator_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > > > >, phmap::Less, std::allocator > >, phmap::Less, std::allocator > > > > > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2382:30: /usr/include/c++/14/bits/new_allocator.h:172:33: warning: 'void operator delete(void*, std::size_t)' called on unallocated object 'empty_node' [-Wfree-nonheap-object] 172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:15: /usr/include/parallel_hashmap/btree.h: In function 'void phmap::priv::btree_node::swap(phmap::priv::btree_node*, allocator_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > > > >, phmap::Less, std::allocator > >, phmap::Less, std::allocator > > > > > > > >, 256, false>]': /usr/include/parallel_hashmap/btree.h:1623:44: note: declared here 1623 | static constexpr EmptyNodeType empty_node( | ^~~~~~~~~~ [ 82%] Building CXX object common/alignment/CMakeFiles/alignment.dir/pacbio/g_aligner.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/alignment/CMakeFiles/alignment.dir/pacbio/g_aligner.cpp.o -MF CMakeFiles/alignment.dir/pacbio/g_aligner.cpp.o.d -o CMakeFiles/alignment.dir/pacbio/g_aligner.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/pacbio/g_aligner.cpp In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/pacbio/gap_filler.hpp:15, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/pacbio/gap_filler.cpp:8: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/paths/path_utils.hpp: In instantiation of 'Sequence debruijn_graph::MergeSequences(const Graph&, const std::vector&) [with Graph = DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/pacbio/gap_filler.cpp:18:41: required from here 18 | Sequence merged_seq = MergeSequences(g_, path); | ~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/paths/path_utils.hpp:120:18: warning: variable 'end' set but not used [-Wunused-but-set-variable] 120 | auto end = g.EdgeEnd(continuous_path[i - 1]); | ^~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/pacbio/gap_dijkstra.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/pacbio/gap_filler.hpp:10: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp: In member function 'size_t debruijn_graph::DeBruijnGraph::link_length(VertexId, EdgeId, EdgeId) const': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp:142:5: warning: control reaches end of non-void function [-Wreturn-type] 142 | } | ^ [ 82%] Linking CXX static library libconfigs.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/configs && /usr/bin/cmake -P CMakeFiles/configs.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/configs && /usr/bin/cmake -E cmake_link_script CMakeFiles/configs.dir/link.txt --verbose=1 /usr/bin/ar qc libconfigs.a CMakeFiles/configs.dir/config_struct.cpp.o CMakeFiles/configs.dir/pe_config_struct.cpp.o /usr/bin/ranlib libconfigs.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 82%] Built target configs make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 82%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/loop_detector.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/loop_detector.cpp.o -MF CMakeFiles/path_extend.dir/loop_detector.cpp.o.d -o CMakeFiles/path_extend.dir/loop_detector.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/loop_detector.cpp [ 82%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/loop_traverser.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/loop_traverser.cpp.o -MF CMakeFiles/path_extend.dir/loop_traverser.cpp.o.d -o CMakeFiles/path_extend.dir/loop_traverser.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/loop_traverser.cpp [ 82%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/path_extenders.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/path_extenders.cpp.o -MF CMakeFiles/path_extend.dir/path_extenders.cpp.o.d -o CMakeFiles/path_extend.dir/path_extenders.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/path_extenders.cpp [ 82%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/gap_analyzer.cpp.o [ 82%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pe_resolver.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/gap_analyzer.cpp.o -MF CMakeFiles/path_extend.dir/gap_analyzer.cpp.o.d -o CMakeFiles/path_extend.dir/gap_analyzer.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/gap_analyzer.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pe_resolver.cpp.o -MF CMakeFiles/path_extend.dir/pe_resolver.cpp.o.d -o CMakeFiles/path_extend.dir/pe_resolver.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/pe_resolver.cpp In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/bits/alloc_traits.h:39, from /usr/include/c++/14/ext/alloc_traits.h:34, from /usr/include/c++/14/bits/hashtable_policy.h:39, from /usr/include/c++/14/bits/hashtable.h:35, from /usr/include/c++/14/bits/unordered_map.h:33, from /usr/include/c++/14/unordered_map:41, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/pack.hpp:14, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline/graph_pack.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline/stage.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/repeat_resolving.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/repeat_resolving.cpp:9: In member function 'void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = phmap::priv::Deallocate<8, std::allocator > > > > >(std::allocator > > > >*, void*, size_t)::M]', inlined from 'static void phmap::allocator_traits::deallocate(Alloc&, pointer, size_type) [with Alloc = std::allocator > > > > >(std::allocator > > > >*, void*, size_t)::M>]' at /usr/include/parallel_hashmap/phmap_base.h:1487:21, inlined from 'void phmap::priv::Deallocate(Alloc*, void*, size_t) [with long unsigned int Alignment = 8; Alloc = std::allocator > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:4210:17, inlined from 'void phmap::priv::btree::deallocate(size_type, node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2003:60, inlined from 'void phmap::priv::btree::delete_leaf_node(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2013:23, inlined from 'void phmap::priv::btree::internal_clear(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:3228:29, inlined from 'void phmap::priv::btree::clear() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2859:27, inlined from 'phmap::priv::btree::~btree() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:1704:18, inlined from 'phmap::priv::btree_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_container()' at /usr/include/parallel_hashmap/btree.h:3264:11, inlined from 'phmap::priv::btree_set_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_set_container()' at /usr/include/parallel_hashmap/btree.h:3429:11, inlined from 'phmap::priv::btree_map_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_map_container()' at /usr/include/parallel_hashmap/btree.h:3591:11, inlined from 'phmap::btree_map > >, phmap::Less, std::allocator > > > > >::~btree_map()' at /usr/include/parallel_hashmap/btree.h:3952:15, inlined from 'omnigraph::de::NoLockingConstAdapter > >, phmap::Less, std::allocator > > > > > >::~NoLockingConstAdapter()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info.hpp:567:7, inlined from 'std::pair > >, phmap::Less, std::allocator > > > > > > >::~pair()' at /usr/include/c++/14/bits/stl_pair.h:284:12, inlined from 'void std::__new_allocator<_Tp>::destroy(_Up*) [with _Up = std::pair > >, phmap::Less, std::allocator > > > > > > >; _Tp = std::pair > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/c++/14/bits/new_allocator.h:198:13, inlined from 'static void std::allocator_traits >::destroy(allocator_type&, _Up*) [with _Up = std::pair > >, phmap::Less, std::allocator > > > > > > >; _Tp = std::pair > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/c++/14/bits/alloc_traits.h:597:15, inlined from 'static decltype (std::allocator_traits::destroy(a, p)) phmap::allocator_traits::destroy_impl(int, A&, T*) [with A = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; T = std::pair > >, phmap::Less, std::allocator > > > > > > >; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:1546:42, inlined from 'static void phmap::allocator_traits::destroy(Alloc&, T*) [with T = std::pair > >, phmap::Less, std::allocator > > > > > > >; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:1504:21, inlined from 'static void phmap::priv::map_slot_policy::swap(Allocator*, slot_type*, slot_type*) [with Allocator = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; K = omnigraph::impl::EdgeId; V = omnigraph::de::NoLockingConstAdapter > >, phmap::Less, std::allocator > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:4554:56, inlined from 'static void phmap::priv::common_params::swap(Alloc*, slot_type*, slot_type*) [with Key = omnigraph::impl::EdgeId; Compare = phmap::Less; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; int TargetNodeSize = 256; bool Multi = false; SlotPolicy = phmap::priv::map_slot_policy > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/parallel_hashmap/btree.h:888:30, inlined from 'void phmap::priv::btree_node::swap(phmap::priv::btree_node*, allocator_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > > > >, phmap::Less, std::allocator > >, phmap::Less, std::allocator > > > > > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2382:30: /usr/include/c++/14/bits/new_allocator.h:172:33: warning: 'void operator delete(void*, std::size_t)' called on unallocated object 'empty_node' [-Wfree-nonheap-object] 172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:15, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/observable_graph.hpp:13, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/edge_index_refiller.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/edge_index.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/sequence_mapper.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/stats/picture_dump.hpp:13: /usr/include/parallel_hashmap/btree.h: In function 'void phmap::priv::btree_node::swap(phmap::priv::btree_node*, allocator_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > > > >, phmap::Less, std::allocator > >, phmap::Less, std::allocator > > > > > > > >, 256, false>]': /usr/include/parallel_hashmap/btree.h:1623:44: note: declared here 1623 | static constexpr EmptyNodeType empty_node( | ^~~~~~~~~~ [ 84%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/overlap_remover.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/overlap_remover.cpp.o -MF CMakeFiles/path_extend.dir/overlap_remover.cpp.o.d -o CMakeFiles/path_extend.dir/overlap_remover.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/overlap_remover.cpp /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/path_extenders.cpp: In member function 'bool path_extend::LoopDetectingPathExtender::TryToResolveHairpin(path_extend::BidirectionalPath&)': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/path_extenders.cpp:124:12: warning: variable 'pin' set but not used [-Wunused-but-set-variable] 124 | EdgeId pin = path[path.Size() - 2]; | ^~~ [ 84%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o -MF CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o.d -o CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/pipeline/launch_support.cpp [ 84%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o -MF CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o.d -o CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/pipeline/launcher.cpp [ 84%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o -MF CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o.d -o CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/pipeline/extenders_logic.cpp [ 84%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp [ 84%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/scaffolder2015/scaffold_graph.cpp [ 85%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.cpp [ 85%] Linking CXX static library libalignment.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/alignment.dir/link.txt --verbose=1 [ 85%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp /usr/bin/ar qc libalignment.a CMakeFiles/alignment.dir/gap_info.cpp.o CMakeFiles/alignment.dir/bwa_index.cpp.o CMakeFiles/alignment.dir/long_read_mapper.cpp.o CMakeFiles/alignment.dir/sequence_mapper_notifier.cpp.o CMakeFiles/alignment.dir/kmer_sequence_mapper.cpp.o CMakeFiles/alignment.dir/pacbio/gap_filler.cpp.o CMakeFiles/alignment.dir/pacbio/gap_dijkstra.cpp.o CMakeFiles/alignment.dir/pacbio/g_aligner.cpp.o /usr/bin/ranlib libalignment.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 85%] Built target alignment make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/DependInfo.cmake "--color=" /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp: In member function 'path_extend::ExtensionChooser::EdgeContainer path_extend::ExtensionChooser2015::FindNextUniqueEdge(path_extend::EdgeId) const': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp:36:19: warning: conversion from 'long unsigned int' to 'double' may change value [-Wconversion] 36 | if (sum < absolute_weight_threshold_) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 85%] Building CXX object common/modules/CMakeFiles/modules.dir/chromosome_remover.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/CMakeFiles/modules.dir/chromosome_remover.cpp.o -MF CMakeFiles/modules.dir/chromosome_remover.cpp.o.d -o CMakeFiles/modules.dir/chromosome_remover.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/chromosome_remover.cpp [ 85%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp [ 85%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp [ 86%] Building CXX object common/modules/CMakeFiles/modules.dir/genome_consistance_checker.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/CMakeFiles/modules.dir/genome_consistance_checker.cpp.o -MF CMakeFiles/modules.dir/genome_consistance_checker.cpp.o.d -o CMakeFiles/modules.dir/genome_consistance_checker.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/genome_consistance_checker.cpp [ 86%] Building CXX object common/modules/CMakeFiles/modules.dir/path_extend/scaff_supplementary.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/CMakeFiles/modules.dir/path_extend/scaff_supplementary.cpp.o -MF CMakeFiles/modules.dir/path_extend/scaff_supplementary.cpp.o.d -o CMakeFiles/modules.dir/path_extend/scaff_supplementary.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/scaff_supplementary.cpp In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/string:43, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/stacktrace.hpp:18, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/verify.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/binary.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/long_read_storage.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_aligning.hpp:11: In member function 'void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = phmap::priv::Deallocate<8, std::allocator > > > > >(std::allocator > > > >*, void*, size_t)::M]', inlined from 'static void phmap::allocator_traits::deallocate(Alloc&, pointer, size_type) [with Alloc = std::allocator > > > > >(std::allocator > > > >*, void*, size_t)::M>]' at /usr/include/parallel_hashmap/phmap_base.h:1487:21, inlined from 'void phmap::priv::Deallocate(Alloc*, void*, size_t) [with long unsigned int Alignment = 8; Alloc = std::allocator > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:4210:17, inlined from 'void phmap::priv::btree::deallocate(size_type, node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2003:60, inlined from 'void phmap::priv::btree::delete_leaf_node(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2013:23, inlined from 'void phmap::priv::btree::internal_clear(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:3228:29, inlined from 'void phmap::priv::btree::clear() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2859:27, inlined from 'phmap::priv::btree::~btree() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:1704:18, inlined from 'phmap::priv::btree_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_container()' at /usr/include/parallel_hashmap/btree.h:3264:11, inlined from 'phmap::priv::btree_set_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_set_container()' at /usr/include/parallel_hashmap/btree.h:3429:11, inlined from 'phmap::priv::btree_map_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_map_container()' at /usr/include/parallel_hashmap/btree.h:3591:11, inlined from 'phmap::btree_map > >, phmap::Less, std::allocator > > > > >::~btree_map()' at /usr/include/parallel_hashmap/btree.h:3952:15, inlined from 'omnigraph::de::NoLockingConstAdapter > >, phmap::Less, std::allocator > > > > > >::~NoLockingConstAdapter()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info.hpp:567:7, inlined from 'std::pair > >, phmap::Less, std::allocator > > > > > > >::~pair()' at /usr/include/c++/14/bits/stl_pair.h:284:12, inlined from 'void std::__new_allocator<_Tp>::destroy(_Up*) [with _Up = std::pair > >, phmap::Less, std::allocator > > > > > > >; _Tp = std::pair > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/c++/14/bits/new_allocator.h:198:13, inlined from 'static void std::allocator_traits >::destroy(allocator_type&, _Up*) [with _Up = std::pair > >, phmap::Less, std::allocator > > > > > > >; _Tp = std::pair > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/c++/14/bits/alloc_traits.h:597:15, inlined from 'static decltype (std::allocator_traits::destroy(a, p)) phmap::allocator_traits::destroy_impl(int, A&, T*) [with A = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; T = std::pair > >, phmap::Less, std::allocator > > > > > > >; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:1546:42, inlined from 'static void phmap::allocator_traits::destroy(Alloc&, T*) [with T = std::pair > >, phmap::Less, std::allocator > > > > > > >; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:1504:21, inlined from 'static void phmap::priv::map_slot_policy::swap(Allocator*, slot_type*, slot_type*) [with Allocator = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; K = omnigraph::impl::EdgeId; V = omnigraph::de::NoLockingConstAdapter > >, phmap::Less, std::allocator > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:4554:56, inlined from 'static void phmap::priv::common_params::swap(Alloc*, slot_type*, slot_type*) [with Key = omnigraph::impl::EdgeId; Compare = phmap::Less; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; int TargetNodeSize = 256; bool Multi = false; SlotPolicy = phmap::priv::map_slot_policy > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/parallel_hashmap/btree.h:888:30, inlined from 'void phmap::priv::btree_node::swap(phmap::priv::btree_node*, allocator_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > > > >, phmap::Less, std::allocator > >, phmap::Less, std::allocator > > > > > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2382:30: /usr/include/c++/14/bits/new_allocator.h:172:33: warning: 'void operator delete(void*, std::size_t)' called on unallocated object 'empty_node' [-Wfree-nonheap-object] 172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:15: /usr/include/parallel_hashmap/btree.h: In function 'void phmap::priv::btree_node::swap(phmap::priv::btree_node*, allocator_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > > > >, phmap::Less, std::allocator > >, phmap::Less, std::allocator > > > > > > > >, 256, false>]': /usr/include/parallel_hashmap/btree.h:1623:44: note: declared here 1623 | static constexpr EmptyNodeType empty_node( | ^~~~~~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/stats/picture_dump.hpp:18, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/path_visualizer.hpp:13, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/pipeline/launcher.cpp:12: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:30:10: required from here 30 | bool Load(const std::string &basename, Graph &graph) override { | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:31:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 31 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:43:10: required from here 43 | bool BinRead(std::istream &is, Graph &graph) override { | ^~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:44:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 44 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:10: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:47:10: required from here 47 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:61:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 61 | auto new_id = graph.AddVertex(typename Graph::VertexData(graph.k()), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:83:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 83 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp: In member function 'virtual path_extend::Connections path_extend::LongReadsLibConnectionCondition::ConnectedWith(path_extend::EdgeId, const path_extend::ScaffoldingUniqueEdgeStorage&) const': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp:118:28: warning: conversion from 'long unsigned int' to 'double' may change value [-Wconversion] 118 | if (iter->second < min_read_count_) { | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/observable_graph.hpp:13, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/chromosome_remover.hpp:8, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/chromosome_remover.cpp:6: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 508 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/chromosome_remover.cpp:40:58: required from here 40 | for (auto it = g.SmartVertexBegin(); ! it.IsEnd(); ++it) { | ^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 508 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/chromosome_remover.cpp:137:64: required from here 137 | for (auto iter = graph.SmartEdgeBegin(); ! iter.IsEnd(); ++iter) { | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/chromosome_remover.cpp:21: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info.hpp: In instantiation of 'void omnigraph::de::PairedIndexHandler::HandleMerge(const std::vector&, EdgeId) [with G = debruijn_graph::DeBruijnGraph; Traits = omnigraph::de::PointTraits; Container = omnigraph::de::const_btree_map; typename Graph::EdgeId = omnigraph::impl::EdgeId; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info.hpp:633:18: required from here 633 | virtual void HandleMerge(const std::vector &old_edges, EdgeId new_edge) override { | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info.hpp:674:53: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'float' may change value [-Wconversion] 674 | if (paired_index_.graph().length(new_edge) > point.d && new_edge != next) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ [ 86%] Linking CXX static library libspades-stages.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/cmake -P CMakeFiles/spades-stages.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-stages.dir/link.txt --verbose=1 /usr/bin/ar qc libspades-stages.a "CMakeFiles/spades-stages.dir/gap_closer.cpp.o" "CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o" "CMakeFiles/spades-stages.dir/pair_info_count.cpp.o" "CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o" "CMakeFiles/spades-stages.dir/distance_estimation.cpp.o" "CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o" "CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o" "CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o" "CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o" "CMakeFiles/spades-stages.dir/extract_domains.cpp.o" "CMakeFiles/spades-stages.dir/domain_matcher.cpp.o" "CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o" "CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o" "CMakeFiles/spades-stages.dir/load_graph.cpp.o" "CMakeFiles/spades-stages.dir/domain_graph.cpp.o" "CMakeFiles/spades-stages.dir/wastewater_disentangle.cpp.o" /usr/bin/ranlib libspades-stages.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 86%] Built target spades-stages [ 86%] Linking CXX static library libpath_extend.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/cmake -P CMakeFiles/path_extend.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/cmake -E cmake_link_script CMakeFiles/path_extend.dir/link.txt --verbose=1 [ 86%] Linking CXX static library libmodules.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules && /usr/bin/cmake -P CMakeFiles/modules.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/modules.dir/link.txt --verbose=1 /usr/bin/ar qc libpath_extend.a CMakeFiles/path_extend.dir/loop_detector.cpp.o CMakeFiles/path_extend.dir/loop_traverser.cpp.o CMakeFiles/path_extend.dir/gap_analyzer.cpp.o CMakeFiles/path_extend.dir/path_extenders.cpp.o CMakeFiles/path_extend.dir/pe_resolver.cpp.o CMakeFiles/path_extend.dir/overlap_remover.cpp.o CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o /usr/bin/ranlib libpath_extend.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 86%] Built target path_extend make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/depend /usr/bin/ar qc libmodules.a CMakeFiles/modules.dir/chromosome_remover.cpp.o CMakeFiles/modules.dir/genome_consistance_checker.cpp.o CMakeFiles/modules.dir/path_extend/scaff_supplementary.cpp.o /usr/bin/ranlib libmodules.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline/CMakeFiles/pipeline.dir/DependInfo.cmake "--color=" [ 86%] Built target modules make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/depend make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/DependInfo.cmake "--color=" [ 86%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/graph_pack.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/pipeline/CMakeFiles/pipeline.dir/graph_pack.cpp.o -MF CMakeFiles/pipeline.dir/graph_pack.cpp.o.d -o CMakeFiles/pipeline.dir/graph_pack.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline/graph_pack.cpp make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/build [ 86%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/graph_pack_helpers.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/pipeline/CMakeFiles/pipeline.dir/graph_pack_helpers.cpp.o -MF CMakeFiles/pipeline.dir/graph_pack_helpers.cpp.o.d -o CMakeFiles/pipeline.dir/graph_pack_helpers.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline/graph_pack_helpers.cpp make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 86%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/sequence_mapper_gp_api.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/pipeline/CMakeFiles/pipeline.dir/sequence_mapper_gp_api.cpp.o -MF CMakeFiles/pipeline.dir/sequence_mapper_gp_api.cpp.o.d -o CMakeFiles/pipeline.dir/sequence_mapper_gp_api.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline/sequence_mapper_gp_api.cpp [ 86%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/stage.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/pipeline/CMakeFiles/pipeline.dir/stage.cpp.o -MF CMakeFiles/pipeline.dir/stage.cpp.o.d -o CMakeFiles/pipeline.dir/stage.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline/stage.cpp [ 86%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/distance_estimation.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/paired_info/CMakeFiles/paired_info.dir/distance_estimation.cpp.o -MF CMakeFiles/paired_info.dir/distance_estimation.cpp.o.d -o CMakeFiles/paired_info.dir/distance_estimation.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/distance_estimation.cpp [ 86%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/paired_info/CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o -MF CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o.d -o CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/weighted_distance_estimation.cpp [ 86%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/paired_info/CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o -MF CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o.d -o CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/smoothing_distance_estimation.cpp [ 86%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/paired_info_utils.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/paired_info/CMakeFiles/paired_info.dir/paired_info_utils.cpp.o -MF CMakeFiles/paired_info.dir/paired_info_utils.cpp.o.d -o CMakeFiles/paired_info.dir/paired_info_utils.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info_utils.cpp [ 86%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/distance_estimation_utils.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/paired_info/CMakeFiles/paired_info.dir/distance_estimation_utils.cpp.o -MF CMakeFiles/paired_info.dir/distance_estimation_utils.cpp.o.d -o CMakeFiles/paired_info.dir/distance_estimation_utils.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/distance_estimation_utils.cpp In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline/stage.cpp:13: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:30:10: required from here 30 | bool Load(const std::string &basename, Graph &graph) override { | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:31:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 31 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:43:10: required from here 43 | bool BinRead(std::istream &is, Graph &graph) override { | ^~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:44:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 44 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:10: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:47:10: required from here 47 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:61:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 61 | auto new_id = graph.AddVertex(typename Graph::VertexData(graph.k()), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:83:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 83 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/split_path_constructor.hpp:18, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/pair_info_improver.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/distance_estimation_utils.cpp:12: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/paths/path_utils.hpp: In instantiation of 'std::vector debruijn_graph::GetCommonPathsEnd(const Graph&, typename Graph::EdgeId, typename Graph::EdgeId, size_t, size_t, typename omnigraph::DijkstraHelper::BoundedDijkstra&) [with Graph = DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId; typename Graph::EdgeId = omnigraph::impl::EdgeId; size_t = long unsigned int; typename omnigraph::DijkstraHelper::BoundedDijkstra = omnigraph::Dijkstra, omnigraph::BoundProcessChecker, omnigraph::BoundPutChecker, omnigraph::ForwardNeighbourIteratorFactory, long unsigned int>, false, long unsigned int>]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/split_path_constructor.hpp:104:64: required from 'std::vector > debruijn_graph::SplitPathConstructor::ConvertPIToSplitPaths(EdgeId, omnigraph::de::PairedInfoIndexT&, double, double) const [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId; omnigraph::de::PairedInfoIndexT = omnigraph::de::PairedIndex]' 104 | std::vector common_part = GetCommonPathsEnd(graph_, cur_edge, cur_info.second, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 105 | (size_t) (cur_info.d() - cur_info.var()), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 106 | (size_t) (cur_info.d() + cur_info.var()), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 107 | dijkstra); | ~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/pair_info_improver.hpp:176:55: required from 'size_t debruijn_graph::PairInfoImprover::FillMissing(unsigned int) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 176 | auto paths = spc.ConvertPIToSplitPaths(e, index_, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ 177 | lib_.data().mean_insert_size, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 178 | lib_.data().insert_size_deviation); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/pair_info_improver.hpp:63:37: required from 'void debruijn_graph::PairInfoImprover::CorrectPairedInfo(unsigned int) [with Graph = debruijn_graph::DeBruijnGraph]' 63 | missing_paired_info_count = FillMissing(nthreads); | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/pair_info_improver.hpp:54:9: required from 'void debruijn_graph::PairInfoImprover::ImprovePairedInfo(unsigned int) [with Graph = debruijn_graph::DeBruijnGraph]' 54 | CorrectPairedInfo(num_threads); | ^~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/distance_estimation_utils.cpp:144:94: required from here 144 | PairInfoImprover(graph, clustered_index, lib, max_repeat_length).ImprovePairedInfo(omp_get_max_threads()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/paths/path_utils.hpp:31:20: warning: unused parameter 'min_dist' [-Wunused-parameter] 31 | size_t min_dist, | ~~~~~~~^~~~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline/graph_pack.cpp:13: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/kmer_mapper.hpp: In instantiation of 'void debruijn_graph::KmerMapper::HandleGlue(EdgeId, EdgeId, EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/kmer_mapper.hpp:148:10: required from here 148 | void HandleGlue(EdgeId new_edge, EdgeId edge1, EdgeId edge2) override { | ^~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/kmer_mapper.hpp:148:28: warning: unused parameter 'new_edge' [-Wunused-parameter] 148 | void HandleGlue(EdgeId new_edge, EdgeId edge1, EdgeId edge2) override { | ~~~~~~~^~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/string:43, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/index_point.hpp:13, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/histogram.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info_buffer.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/distance_estimation.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/distance_estimation_utils.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/distance_estimation_utils.cpp:8: In member function 'void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = phmap::priv::Deallocate<8, std::allocator > > > > >(std::allocator > > > >*, void*, size_t)::M]', inlined from 'static void phmap::allocator_traits::deallocate(Alloc&, pointer, size_type) [with Alloc = std::allocator > > > > >(std::allocator > > > >*, void*, size_t)::M>]' at /usr/include/parallel_hashmap/phmap_base.h:1487:21, inlined from 'void phmap::priv::Deallocate(Alloc*, void*, size_t) [with long unsigned int Alignment = 8; Alloc = std::allocator > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:4210:17, inlined from 'void phmap::priv::btree::deallocate(size_type, node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2003:60, inlined from 'void phmap::priv::btree::delete_leaf_node(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2013:23, inlined from 'void phmap::priv::btree::internal_clear(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:3228:29, inlined from 'void phmap::priv::btree::clear() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2859:27, inlined from 'phmap::priv::btree::~btree() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:1704:18, inlined from 'phmap::priv::btree_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_container()' at /usr/include/parallel_hashmap/btree.h:3264:11, inlined from 'phmap::priv::btree_set_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_set_container()' at /usr/include/parallel_hashmap/btree.h:3429:11, inlined from 'phmap::priv::btree_map_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_map_container()' at /usr/include/parallel_hashmap/btree.h:3591:11, inlined from 'phmap::btree_map > >, phmap::Less, std::allocator > > > > >::~btree_map()' at /usr/include/parallel_hashmap/btree.h:3952:15, inlined from 'omnigraph::de::NoLockingConstAdapter > >, phmap::Less, std::allocator > > > > > >::~NoLockingConstAdapter()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info.hpp:567:7, inlined from 'omnigraph::de::PairedIndex::~PairedIndex()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info.hpp:26:7, inlined from 'void std::__new_allocator<_Tp>::destroy(_Up*) [with _Up = omnigraph::de::PairedIndex; _Tp = omnigraph::de::PairedIndex]' at /usr/include/c++/14/bits/new_allocator.h:198:13, inlined from 'static void std::allocator_traits >::destroy(allocator_type&, _Up*) [with _Up = omnigraph::de::PairedIndex; _Tp = omnigraph::de::PairedIndex]' at /usr/include/c++/14/bits/alloc_traits.h:597:15, inlined from 'void std::__relocate_object_a(_Tp*, _Up*, _Allocator&) [with _Tp = omnigraph::de::PairedIndex; _Up = omnigraph::de::PairedIndex; _Allocator = allocator >]' at /usr/include/c++/14/bits/stl_uninitialized.h:1076:24, inlined from '_ForwardIterator std::__relocate_a_1(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = omnigraph::de::PairedIndex*; _ForwardIterator = omnigraph::de::PairedIndex*; _Allocator = allocator >]' at /usr/include/c++/14/bits/stl_uninitialized.h:1103:26, inlined from '_ForwardIterator std::__relocate_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = omnigraph::de::PairedIndex*; _ForwardIterator = omnigraph::de::PairedIndex*; _Allocator = allocator >]' at /usr/include/c++/14/bits/stl_uninitialized.h:1145:33, inlined from 'static std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_S_relocate(pointer, pointer, pointer, _Tp_alloc_type&) [with _Tp = omnigraph::de::PairedIndex; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/stl_vector.h:509:26, inlined from 'void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {const debruijn_graph::DeBruijnGraph&}; _Tp = omnigraph::de::PairedIndex; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/vector.tcc:647:32: /usr/include/c++/14/bits/new_allocator.h:172:33: warning: 'void operator delete(void*, std::size_t)' called on unallocated object 'empty_node' [-Wfree-nonheap-object] 172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info.hpp:17: /usr/include/parallel_hashmap/btree.h: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {const debruijn_graph::DeBruijnGraph&}; _Tp = omnigraph::de::PairedIndex; _Alloc = std::allocator >]': /usr/include/parallel_hashmap/btree.h:1623:44: note: declared here 1623 | static constexpr EmptyNodeType empty_node( | ^~~~~~~~~~ [ 86%] Linking CXX static library libpipeline.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/cmake -P CMakeFiles/pipeline.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/cmake -E cmake_link_script CMakeFiles/pipeline.dir/link.txt --verbose=1 /usr/bin/ar qc libpipeline.a CMakeFiles/pipeline.dir/graph_pack.cpp.o CMakeFiles/pipeline.dir/graph_pack_helpers.cpp.o CMakeFiles/pipeline.dir/sequence_mapper_gp_api.cpp.o CMakeFiles/pipeline.dir/stage.cpp.o /usr/bin/ranlib libpipeline.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 86%] Built target pipeline make -f common/stages/CMakeFiles/stages.dir/build.make common/stages/CMakeFiles/stages.dir/depend make -f projects/ionhammer/CMakeFiles/spades-ionhammer.dir/build.make projects/ionhammer/CMakeFiles/spades-ionhammer.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/stages /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/stages/CMakeFiles/stages.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer/CMakeFiles/spades-ionhammer.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/stages/CMakeFiles/stages.dir/build.make common/stages/CMakeFiles/stages.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f projects/ionhammer/CMakeFiles/spades-ionhammer.dir/build.make projects/ionhammer/CMakeFiles/spades-ionhammer.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 86%] Building CXX object common/stages/CMakeFiles/stages.dir/read_conversion.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_data.cpp.o -MF CMakeFiles/spades-ionhammer.dir/kmer_data.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/kmer_data.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/kmer_data.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/stages/CMakeFiles/stages.dir/construction.cpp.o -MF CMakeFiles/stages.dir/construction.cpp.o.d -o CMakeFiles/stages.dir/construction.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/construction.cpp [ 87%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/stages/CMakeFiles/stages.dir/simplification.cpp.o -MF CMakeFiles/stages.dir/simplification.cpp.o.d -o CMakeFiles/stages.dir/simplification.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=16777216UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o -MF CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/subcluster.cpp [ 87%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o [ 87%] Building CXX object common/stages/CMakeFiles/stages.dir/ss_edge_split.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=16777216UL 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-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o -MF CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/err_helper_table.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/stages/CMakeFiles/stages.dir/ss_edge_split.cpp.o -MF CMakeFiles/stages.dir/ss_edge_split.cpp.o.d -o CMakeFiles/stages.dir/ss_edge_split.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/ss_edge_split.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=16777216UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o -MF CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/config_struct.cpp [ 89%] Building CXX object common/stages/CMakeFiles/stages.dir/genomic_info_filler.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/stages/CMakeFiles/stages.dir/genomic_info_filler.cpp.o -MF CMakeFiles/stages.dir/genomic_info_filler.cpp.o.d -o CMakeFiles/stages.dir/genomic_info_filler.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/genomic_info_filler.cpp [ 89%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_helpers.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=16777216UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_helpers.cpp.o -MF CMakeFiles/spades-ionhammer.dir/kmer_helpers.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/kmer_helpers.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/kmer_helpers.cpp [ 89%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/BaseHypothesisEvaluator.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=16777216UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/BaseHypothesisEvaluator.cpp.o -MF CMakeFiles/spades-ionhammer.dir/seqeval/BaseHypothesisEvaluator.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/seqeval/BaseHypothesisEvaluator.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp: In function 'void BaseHypothesisEvaluator(BamTools::BamAlignment&, const std::string&, const std::string&, float&, float&, int)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp:33:56: warning: conversion from 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} to 'int' may change value [-Wconversion] 33 | if (not GetBamTags(alignment, flow_order_str.length(), measurements, phase_params, start_flow)) | ~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp:35:34: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'int' may change value [-Wconversion] 35 | num_flows = measurements.size(); | ~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp:53:57: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'unsigned int' may change value [-Wconversion] 53 | unsigned int prefix_size = master_read.sequence.size(); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp: In function 'void RevComplementInPlace(std::string&)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp:299:32: warning: conversion from 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} to 'int' may change value [-Wconversion] 299 | int backward_idx = seq.size()-1; | ~~~~~~~~~~^~ [ 90%] Linking CXX static library libpaired_info.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/cmake -P CMakeFiles/paired_info.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/cmake -E cmake_link_script CMakeFiles/paired_info.dir/link.txt --verbose=1 [ 91%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/TreephaserLite.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=16777216UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/TreephaserLite.cpp.o -MF CMakeFiles/spades-ionhammer.dir/seqeval/TreephaserLite.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/seqeval/TreephaserLite.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/TreephaserLite.cpp [ 91%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/main.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=16777216UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/main.cpp.o -MF CMakeFiles/spades-ionhammer.dir/main.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/main.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/main.cpp /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/TreephaserLite.cpp: In member function 'void TreephaserLite::SetModelParameters(double, double, double)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/TreephaserLite.cpp:92:76: warning: conversion from 'double' to '__gnu_cxx::__alloc_traits, float>::value_type' {aka 'float'} may change value [-Wfloat-conversion] 92 | transition_base_[nuc][flow] = nuc_avaliability[nuc] * (1-droop_rate) * (1-incomplete_extension_rate); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/TreephaserLite.cpp:93:63: warning: conversion from 'double' to '__gnu_cxx::__alloc_traits, float>::value_type' {aka 'float'} may change value [-Wfloat-conversion] 93 | transition_flow_[nuc][flow] = (1-nuc_avaliability[nuc]) + nuc_avaliability[nuc] * (1-droop_rate) * incomplete_extension_rate; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/TreephaserLite.cpp: In member function 'void TreephaserLite::WindowedNormalize(BasecallerRead&, int, int) const': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/TreephaserLite.cpp:104:45: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'int' may change value [-Wconversion] 104 | int num_flows = read.raw_measurements.size(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/TreephaserLite.cpp:134:52: warning: conversion from 'int' to 'float' may change value [-Wconversion] 134 | float delta = (next_normalizer - normalizer) / window_size; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/TreephaserLite.cpp:173:52: warning: conversion from 'int' to 'float' may change value [-Wconversion] 173 | float delta = (next_normalizer - normalizer) / window_size; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/TreephaserLite.cpp: In member function 'void TreephaserLite::Solve(BasecallerRead&, int, int)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/TreephaserLite.cpp:357:38: warning: conversion from 'double' to 'float' changes value from '1.0e+20' to '1.00000002e+20f' [-Wfloat-conversion] 357 | float sum_of_squares_upper_bound = 1e20; //max_flows; // Squared distance of solution to measurements | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/TreephaserLite.cpp:416:35: warning: conversion from 'double' to 'float' changes value from '-1.0000000000000001e-1' to '-1.00000001e-1f' [-Wfloat-conversion] 416 | float max_per_flow_metric = -0.1; | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/TreephaserLite.cpp:521:72: warning: conversion from 'double' to 'float' may change value [-Wfloat-conversion] 521 | child->per_flow_metric = (child->path_metric + 0.5 * penalty1) / child->flow; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ [ 91%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/reference.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=16777216UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/reference.cpp.o -MF CMakeFiles/spades-ionhammer.dir/reference.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/reference.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/reference.cpp /usr/bin/ar qc libpaired_info.a CMakeFiles/paired_info.dir/distance_estimation.cpp.o CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o CMakeFiles/paired_info.dir/paired_info_utils.cpp.o CMakeFiles/paired_info.dir/distance_estimation_utils.cpp.o /usr/bin/ranlib libpaired_info.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 91%] Built target paired_info [ 91%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_metrics.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=16777216UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_metrics.cpp.o -MF CMakeFiles/spades-ionhammer.dir/quality_metrics.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/quality_metrics.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/quality_metrics.cpp In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/hkmer.hpp:14, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/kmer_data.hpp:18, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/kmer_data.cpp:9: /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/HSeq.hpp: In instantiation of 'static size_t hammer::HSeq::GetDataSize(size_t) [with long unsigned int N = 16; size_t = long unsigned int]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/kmer_mph/kmer_index_builder.hpp:174:52: required from 'void kmers::KMerDiskStorage::merge() [with S = hammer::HSeq<16>; traits = kmers::kmer_index_traits >]' 174 | BucketStorage bucket(*entry, Seq::GetDataSize(k_), false); | ~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/kmer_mph/kmer_index_builder.hpp:461:25: required from 'auto kmers::KMerIndexBuilder::BuildIndex(Index&, kmers::KMerCounter&, bool) [with Index = kmers::KMerIndex > >; typename Index::KMerSeq = hammer::HSeq<16>]' 461 | kmer_storage.merge(); | ~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/kmer_data.cpp:173:102: required from here 173 | auto res = kmers::KMerIndexBuilder(num_files_, cfg::get().max_nthreads).BuildIndex(data.index_, counter, false); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/HSeq.hpp:94:36: warning: unused parameter 'size' [-Wunused-parameter] 94 | static size_t GetDataSize(size_t size) { | ~~~~~~~^~~~ [ 91%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=16777216UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o -MF CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/quality_thresholds_estimator.cpp [ 91%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=16777216UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o -MF CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/hamcluster_1.cpp [ 92%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=16777216UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o -MF CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/gamma_poisson_model.cpp [ 92%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=16777216UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o -MF CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/normal_quality_model.cpp In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/graph_processing_algorithm.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification.cpp:12: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 508 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/graph_processing_algorithm.hpp:60:87: required from 'bool omnigraph::EdgeProcessingAlgorithm::Run(const Priority&, ProceedConditionT) [with Priority = adt::identity; Graph = debruijn_graph::DeBruijnGraph; ProceedConditionT = func::TypedPredicate]' 60 | for (auto it = g_.SmartEdgeBegin(priority, conjugate_symmetry_); !it.IsEnd(); ++it) { | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification.cpp:349:94: required from here 349 | SelfConjugateDisruptor(g_, cfg::get().max_repeat_length, removal_handler_).Run(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap >]' 508 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/parallel_processing.hpp:378:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator; size_t = long unsigned int]' 378 | for (; !it_.IsEnd(); ++it_) { | ^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification.cpp:366:28: required from here 366 | cov_cleaner.Run(); | ~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 508 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/parallel_processing.hpp:378:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity; size_t = long unsigned int]' 378 | for (; !it_.IsEnd(); ++it_) { | ^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/compressor.hpp:130:26: required from 'size_t omnigraph::CompressAllVertices(Graph&, size_t, bool) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 130 | return compressor.Run(); | ~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification.cpp:487:24: required from here 487 | CompressAllVertices(gp.get_mutable()); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap >]' 508 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/graph_processing_algorithm.hpp:60:87: required from 'bool omnigraph::EdgeProcessingAlgorithm::Run(const Priority&, ProceedConditionT) [with Priority = omnigraph::LengthComparator; Graph = debruijn_graph::DeBruijnGraph; ProceedConditionT = func::TypedPredicate]' 60 | for (auto it = g_.SmartEdgeBegin(priority, conjugate_symmetry_); !it.IsEnd(); ++it) { | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/single_cell_simplification.hpp:45:38: required from 'bool debruijn::simplification::RemoveErroneousEdgesInLengthOrder(Graph&, func::TypedPredicate, size_t, std::function) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId; size_t = long unsigned int; typename Graph::EdgeId = omnigraph::impl::EdgeId]' 45 | return erroneous_edge_remover.Run(omnigraph::LengthComparator(g), | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 46 | omnigraph::LengthUpperBound(g, max_length)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/single_cell_simplification.hpp:63:45: required from 'bool debruijn::simplification::TopologyRemoveErroneousEdges(Graph&, const debruijn_graph::config::debruijn_config::simplification::topology_based_ec_remover&, std::function) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId]' 63 | return RemoveErroneousEdgesInLengthOrder(g, condition, max_length, removal_handler); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification.cpp:85:52: required from here 85 | bool changed = TopologyRemoveErroneousEdges(g_, simplif_cfg_.tec, handler); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_tip_clipper.hpp:14, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/graph_simplification.hpp:18, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification.cpp:18: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/dominated_set_finder.hpp: In instantiation of 'Range omnigraph::DominatedSetFinder::NeighbourDistanceRange(VertexId, bool) const [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/dominated_set_finder.hpp:107:23: required from 'bool omnigraph::DominatedSetFinder::FillDominated() [with Graph = debruijn_graph::DeBruijnGraph]' 107 | Range r = NeighbourDistanceRange(v); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_tip_clipper.hpp:95:33: required from 'omnigraph::GraphComponent omnigraph::ComplexTipFinder::operator()(VertexId) const [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' 95 | if (finder.FillDominated()) { | ~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_tip_clipper.hpp:150:49: required from 'omnigraph::ComplexTipClipper::ComplexTipClipper(Graph&, double, size_t, size_t, size_t, const std::filesystem::__cxx11::path&, HandlerF) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int; HandlerF = std::function, std::allocator >&)>]' 150 | [&](VertexId v) {return !finder_(v).empty();}, chunk_cnt); | ~~~~~~~^~~ /usr/include/c++/14/bits/stl_construct.h:119:7: required from 'void std::_Construct(_Tp*, _Args&& ...) [with _Tp = omnigraph::ComplexTipClipper; _Args = {debruijn_graph::DeBruijnGraph&, double&, long unsigned int&, long unsigned int, long unsigned int, const char (&)[1], function, allocator >&)>&}]' 119 | ::new((void*)__p) _Tp(std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/alloc_traits.h:706:19: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /usr/include/c++/14/bits/shared_ptr_base.h:969:16: required from 'std::__shared_count<_Lp>::__shared_count(_Tp*&, std::_Sp_alloc_shared_tag<_Alloc>, _Args&& ...) [with _Tp = omnigraph::ComplexTipClipper; _Alloc = std::allocator; _Args = {debruijn_graph::DeBruijnGraph&, double&, long unsigned int&, long unsigned int, long unsigned int, const char (&)[1], std::function, std::allocator >&)>&}; __gnu_cxx::_Lock_policy _Lp = __gnu_cxx::_S_atomic]' 969 | auto __pi = ::new (__mem) | ^~~~~~~~~~~~~ 970 | _Sp_cp_type(__a._M_a, std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/shared_ptr_base.h:1713:14: required from 'std::__shared_ptr<_Tp, _Lp>::__shared_ptr(std::_Sp_alloc_shared_tag<_Tp>, _Args&& ...) [with _Alloc = std::allocator; _Args = {debruijn_graph::DeBruijnGraph&, double&, long unsigned int&, long unsigned int, long unsigned int, const char (&)[1], std::function, std::allocator >&)>&}; _Tp = omnigraph::ComplexTipClipper; __gnu_cxx::_Lock_policy _Lp = __gnu_cxx::_S_atomic]' 1713 | : _M_ptr(), _M_refcount(_M_ptr, __tag, std::forward<_Args>(__args)...) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/shared_ptr.h:463:59: required from 'std::shared_ptr<_Tp>::shared_ptr(std::_Sp_alloc_shared_tag<_Tp>, _Args&& ...) [with _Alloc = std::allocator; _Args = {debruijn_graph::DeBruijnGraph&, double&, long unsigned int&, long unsigned int, long unsigned int, const char (&)[1], std::function, std::allocator >&)>&}; _Tp = omnigraph::ComplexTipClipper]' 463 | : __shared_ptr<_Tp>(__tag, std::forward<_Args>(__args)...) | ^ /usr/include/c++/14/bits/shared_ptr.h:1007:14: required from 'std::shared_ptr::value), _Tp>::type> std::make_shared(_Args&& ...) [with _Tp = omnigraph::ComplexTipClipper; _Args = {debruijn_graph::DeBruijnGraph&, double&, long unsigned int&, long unsigned int, long unsigned int, const char (&)[1], function, allocator >&)>&}; typename enable_if<(! is_array<_Tp>::value), _Tp>::type = omnigraph::ComplexTipClipper]' 1007 | return shared_ptr<_Tp>(_Sp_alloc_shared_tag<_Alloc>{__a}, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1008 | std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/graph_simplification.hpp:501:65: required from 'omnigraph::AlgoPtr debruijn::simplification::ComplexTipClipperInstance(Graph&, debruijn_graph::config::debruijn_config::simplification::complex_tip_clipper, const SimplifInfoContainer&, typename omnigraph::ComponentRemover::HandlerF) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::AlgoPtr = std::shared_ptr >; typename omnigraph::ComponentRemover::HandlerF = std::function, std::allocator >&)>]' 501 | return std::make_shared>(g, ctc_conf.max_relative_coverage, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | ctc_conf.max_edge_len, | ~~~~~~~~~~~~~~~~~~~~~~ 503 | parser.max_length_bound(), info.chunk_cnt(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 504 | "", removal_handler); | ~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification.cpp:268:42: required from here 268 | ComplexTipClipperInstance(g_, simplif_cfg_.complex_tc, info_container_, set_removal_handler_f), | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/dominated_set_finder.hpp:50:51: warning: unused parameter 'dominated_only' [-Wunused-parameter] 50 | Range NeighbourDistanceRange(VertexId v, bool dominated_only = true) const { | ~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/chimera_stats.hpp:13, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/graph_simplification.hpp:12: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp: In instantiation of 'void omnigraph::simplification::relative_coverage::Component::RemoveFromBorder(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp:85:9: required from 'void omnigraph::simplification::relative_coverage::Component::MakeInner(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' 85 | RemoveFromBorder(v); | ^~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp:506:37: required from 'bool omnigraph::simplification::relative_coverage::component_remover::InnerComponentSearcher::FindComponent() [with Graph = debruijn_graph::DeBruijnGraph]' 506 | component_.MakeInner(v); | ~~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp:669:49: required from 'std::optional > omnigraph::simplification::relative_coverage::component_remover::RelativeCovComponentFinder::operator()(EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]' 669 | if (component_searcher.FindComponent()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp:722:61: required from 'omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover::RelativeCoverageComponentRemover(Graph&, size_t, const omnigraph::FlankingCoverage&, double, size_t, size_t, size_t, double, HandlerF, size_t, std::filesystem::__cxx11::path) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int; HandlerF = std::function, std::allocator >&)>]' 722 | [&](EdgeId e) { return static_cast(finder_(e)); }, chunk_cnt); | ~~~~~~~^~~ /usr/include/c++/14/bits/stl_construct.h:119:7: required from 'void std::_Construct(_Tp*, _Args&& ...) [with _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, function, allocator >&)>&, const long unsigned int&, filesystem::__cxx11::path&}]' 119 | ::new((void*)__p) _Tp(std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/alloc_traits.h:706:19: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /usr/include/c++/14/bits/shared_ptr_base.h:969:16: required from 'std::__shared_count<_Lp>::__shared_count(_Tp*&, std::_Sp_alloc_shared_tag<_Alloc>, _Args&& ...) [with _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; _Alloc = std::allocator; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::filesystem::__cxx11::path&}; __gnu_cxx::_Lock_policy _Lp = __gnu_cxx::_S_atomic]' 969 | auto __pi = ::new (__mem) | ^~~~~~~~~~~~~ 970 | _Sp_cp_type(__a._M_a, std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/shared_ptr_base.h:1713:14: required from 'std::__shared_ptr<_Tp, _Lp>::__shared_ptr(std::_Sp_alloc_shared_tag<_Tp>, _Args&& ...) [with _Alloc = std::allocator; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::filesystem::__cxx11::path&}; _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; __gnu_cxx::_Lock_policy _Lp = __gnu_cxx::_S_atomic]' 1713 | : _M_ptr(), _M_refcount(_M_ptr, __tag, std::forward<_Args>(__args)...) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/shared_ptr.h:463:59: required from 'std::shared_ptr<_Tp>::shared_ptr(std::_Sp_alloc_shared_tag<_Tp>, _Args&& ...) [with _Alloc = std::allocator; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::filesystem::__cxx11::path&}; _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover]' 463 | : __shared_ptr<_Tp>(__tag, std::forward<_Args>(__args)...) | ^ /usr/include/c++/14/bits/shared_ptr.h:1007:14: required from 'std::shared_ptr::value), _Tp>::type> std::make_shared(_Args&& ...) [with _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, function, allocator >&)>&, const long unsigned int&, filesystem::__cxx11::path&}; typename enable_if<(! is_array<_Tp>::value), _Tp>::type = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover]' 1007 | return shared_ptr<_Tp>(_Sp_alloc_shared_tag<_Alloc>{__a}, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1008 | std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/graph_simplification.hpp:438:49: required from 'omnigraph::AlgoPtr debruijn::simplification::RelativeCoverageComponentRemoverInstance(Graph&, const omnigraph::FlankingCoverage&, const debruijn_graph::config::debruijn_config::simplification::relative_coverage_comp_remover&, const SimplifInfoContainer&, typename omnigraph::ComponentRemover::HandlerF) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::AlgoPtr = std::shared_ptr >; typename omnigraph::ComponentRemover::HandlerF = std::function, std::allocator >&)>]' 437 | return std::make_shared>(g, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 439 | info.chunk_cnt(), | ~~~~~~~~~~~~~~~~~ 440 | flanking_cov, | ~~~~~~~~~~~~~ 441 | rcc_config.coverage_gap, | ~~~~~~~~~~~~~~~~~~~~~~~~ 442 | size_t(double(info.read_length()) * rcc_config.length_coeff), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 443 | size_t(double(info.read_length()) * rcc_config.tip_allowing_length_coeff), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 444 | connecting_path_length_bound, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 445 | max_coverage, | ~~~~~~~~~~~~~ 446 | removal_handler, rcc_config.vertex_count_limit, pics_dir); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification.cpp:257:57: required from here 257 | RelativeCoverageComponentRemoverInstance(g_, flanking_cov, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 258 | simplif_cfg_.rcc, info_container_, set_removal_handler_f), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp:55:16: warning: unused variable 'cnt' [-Wunused-variable] 55 | size_t cnt = border_.erase(v); | ^~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/stats/picture_dump.hpp:18, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification.cpp:13: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:30:10: required from here 30 | bool Load(const std::string &basename, Graph &graph) override { | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:31:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 31 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:43:10: required from here 43 | bool BinRead(std::istream &is, Graph &graph) override { | ^~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:44:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 44 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:10: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:47:10: required from here 47 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:61:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 61 | auto new_id = graph.AddVertex(typename Graph::VertexData(graph.k()), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:83:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 83 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/graph_simplification.hpp:19: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/bulge_remover.hpp: In instantiation of 'omnigraph::ParallelBulgeRemover::SmartEdgeSet omnigraph::ParallelBulgeRemover::RetainIndependentBulges(std::vector&) const [with Graph = debruijn_graph::DeBruijnGraph; SmartEdgeSet = omnigraph::SmartSetIterator >]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/bulge_remover.hpp:721:42: required from 'size_t omnigraph::ParallelBulgeRemover::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 721 | auto interacting_edges = RetainIndependentBulges(bulges); | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/bulge_remover.hpp:678:12: required from here 678 | size_t Run(bool force_primary_launch, double /*iter_run_progress*/) override { | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/bulge_remover.hpp:582:16: warning: unused variable 'total_cnt' [-Wunused-variable] 582 | size_t total_cnt = bulges.size(); | ^~~~~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/graph_simplification.hpp:20: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'bool omnigraph::complex_br::ComponentProjector::SplitComponent() [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:812:14: required from 'bool omnigraph::complex_br::ComponentProjector::ProjectComponent() [with Graph = debruijn_graph::DeBruijnGraph]' 812 | if (!SplitComponent()) { | ^~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1120:44: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::ProcessComponent(omnigraph::complex_br::LocalizedComponent&, size_t) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 1120 | if (!projector.ProjectComponent()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1147:17: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::InnerProcess(VertexId, std::vector&) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId; typename Graph::VertexId = omnigraph::impl::VertexId; typename Graph::VertexId = omnigraph::impl::VertexId]' 1147 | if (ProcessComponent(component, candidate_cnt)) { | ^~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1193:13: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::Process(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' 1193 | if (InnerProcess(v, vertices_to_post_process)) { | ^~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1187:10: required from here 1187 | bool Process(VertexId v) override { | ^~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:776:26: warning: variable 'inner_v' set but not used [-Wunused-but-set-variable] 776 | VertexId inner_v = g_.EdgeEnd(split_res.first); | ^~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'omnigraph::complex_br::ComponentProjector::EdgeId omnigraph::complex_br::ComponentProjector::CorrespondingTreeEdge(EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:823:29: required from 'bool omnigraph::complex_br::ComponentProjector::ProjectComponent() [with Graph = debruijn_graph::DeBruijnGraph]' 823 | EdgeId target = CorrespondingTreeEdge(*it); | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1120:44: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::ProcessComponent(omnigraph::complex_br::LocalizedComponent&, size_t) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 1120 | if (!projector.ProjectComponent()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1147:17: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::InnerProcess(VertexId, std::vector&) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId; typename Graph::VertexId = omnigraph::impl::VertexId; typename Graph::VertexId = omnigraph::impl::VertexId]' 1147 | if (ProcessComponent(component, candidate_cnt)) { | ^~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1193:13: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::Process(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' 1193 | if (InnerProcess(v, vertices_to_post_process)) { | ^~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1187:10: required from here 1187 | bool Process(VertexId v) override { | ^~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:792:16: warning: unused variable 'end_height' [-Wunused-variable] 792 | size_t end_height = component_.avg_distance(g_.EdgeEnd(e)); | ^~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'void omnigraph::complex_br::SkeletonTree::HandleDelete(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:310:10: required from here 310 | void HandleDelete(VertexId v) override { | ^~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:310:32: warning: unused parameter 'v' [-Wunused-parameter] 310 | void HandleDelete(VertexId v) override { | ~~~~~~~~~^ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'void omnigraph::complex_br::SkeletonTree::HandleMerge(const std::vector&, EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:321:10: required from here 321 | void HandleMerge(const std::vector &old_edges, EdgeId /*new_edge*/) override { | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:323:21: warning: variable 'e' set but not used [-Wunused-but-set-variable] 323 | for (EdgeId e : old_edges) { | ^ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'void omnigraph::complex_br::ComponentColoring::HandleGlue(EdgeId, EdgeId, EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:477:18: required from here 477 | virtual void HandleGlue(EdgeId /*new_edge*/, EdgeId edge1, EdgeId edge2) { | ^~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:477:71: warning: unused parameter 'edge2' [-Wunused-parameter] 477 | virtual void HandleGlue(EdgeId /*new_edge*/, EdgeId edge1, EdgeId edge2) { | ~~~~~~~^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'void omnigraph::complex_br::LocalizedComponent::HandleSplit(EdgeId, EdgeId, EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:242:18: required from here 242 | virtual void HandleSplit(EdgeId old_edge, EdgeId new_edge_1, EdgeId /*new_edge_2*/) { | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:245:18: warning: variable 'end' set but not used [-Wunused-but-set-variable] 245 | VertexId end = g_.EdgeEnd(old_edge); | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/main.cpp: In static member function 'static bool hammer::correction::TKMerDataEstimator::stage(hammer_config::HammerStage, hammer_config::HammerStage)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/main.cpp:91:3: warning: control reaches end of non-void function [-Wreturn-type] 91 | } | ^ [ 92%] Linking CXX executable ../../bin/spades-ionhammer cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-ionhammer.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/spades-ionhammer.dir/link.d "CMakeFiles/spades-ionhammer.dir/kmer_data.cpp.o" "CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o" "CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o" "CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o" "CMakeFiles/spades-ionhammer.dir/kmer_helpers.cpp.o" "CMakeFiles/spades-ionhammer.dir/seqeval/BaseHypothesisEvaluator.cpp.o" "CMakeFiles/spades-ionhammer.dir/seqeval/TreephaserLite.cpp.o" "CMakeFiles/spades-ionhammer.dir/main.cpp.o" "CMakeFiles/spades-ionhammer.dir/reference.cpp.o" "CMakeFiles/spades-ionhammer.dir/quality_metrics.cpp.o" "CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o" "CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o" "CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o" "CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-ionhammer ../../common/modules/libmodules.a ../../common/io/libinput.a ../../common/utils/libutils.a ../../common/pipeline/libpipeline.a ../../common/kmer_index/libmph_index.a /usr/lib/x86_64-linux-gnu/libbamtools.so ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/alignment/libalignment.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/bwa/libbwa.a ../../common/modules/path_extend/libpath_extend.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -lssw ../../common/configs/libconfigs.a ../../common/library/liblibrary.a ../../common/io/libinput.a ../../common/io/sam/libsamio.a ../../ext/samtools/libsamtools.a /usr/lib/x86_64-linux-gnu/libbamtools.so ../../common/io/binary/libbinary_io.a ../../_deps/zlib_ng-build/libz.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 92%] Built target spades-ionhammer In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/bits/alloc_traits.h:39, from /usr/include/c++/14/ext/alloc_traits.h:34, from /usr/include/c++/14/bits/hashtable_policy.h:39, from /usr/include/c++/14/bits/hashtable.h:35, from /usr/include/c++/14/bits/unordered_map.h:33, from /usr/include/c++/14/unordered_map:41, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/pack.hpp:14, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline/graph_pack.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline/stage.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification.cpp:9: In member function 'void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = phmap::priv::Deallocate<8, std::allocator > > > > >(std::allocator > > > >*, void*, size_t)::M]', inlined from 'static void phmap::allocator_traits::deallocate(Alloc&, pointer, size_type) [with Alloc = std::allocator > > > > >(std::allocator > > > >*, void*, size_t)::M>]' at /usr/include/parallel_hashmap/phmap_base.h:1487:21, inlined from 'void phmap::priv::Deallocate(Alloc*, void*, size_t) [with long unsigned int Alignment = 8; Alloc = std::allocator > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:4210:17, inlined from 'void phmap::priv::btree::deallocate(size_type, node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2003:60, inlined from 'void phmap::priv::btree::delete_leaf_node(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2013:23, inlined from 'void phmap::priv::btree::internal_clear(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:3228:29, inlined from 'void phmap::priv::btree::clear() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2859:27, inlined from 'phmap::priv::btree::~btree() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:1704:18, inlined from 'phmap::priv::btree_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_container()' at /usr/include/parallel_hashmap/btree.h:3264:11, inlined from 'phmap::priv::btree_set_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_set_container()' at /usr/include/parallel_hashmap/btree.h:3429:11, inlined from 'phmap::priv::btree_map_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_map_container()' at /usr/include/parallel_hashmap/btree.h:3591:11, inlined from 'phmap::btree_map > >, phmap::Less, std::allocator > > > > >::~btree_map()' at /usr/include/parallel_hashmap/btree.h:3952:15, inlined from 'omnigraph::de::NoLockingConstAdapter > >, phmap::Less, std::allocator > > > > > >::~NoLockingConstAdapter()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info.hpp:567:7, inlined from 'std::pair > >, phmap::Less, std::allocator > > > > > > >::~pair()' at /usr/include/c++/14/bits/stl_pair.h:284:12, inlined from 'void std::__new_allocator<_Tp>::destroy(_Up*) [with _Up = std::pair > >, phmap::Less, std::allocator > > > > > > >; _Tp = std::pair > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/c++/14/bits/new_allocator.h:198:13, inlined from 'static void std::allocator_traits >::destroy(allocator_type&, _Up*) [with _Up = std::pair > >, phmap::Less, std::allocator > > > > > > >; _Tp = std::pair > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/c++/14/bits/alloc_traits.h:597:15, inlined from 'static decltype (std::allocator_traits::destroy(a, p)) phmap::allocator_traits::destroy_impl(int, A&, T*) [with A = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; T = std::pair > >, phmap::Less, std::allocator > > > > > > >; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:1546:42, inlined from 'static void phmap::allocator_traits::destroy(Alloc&, T*) [with T = std::pair > >, phmap::Less, std::allocator > > > > > > >; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:1504:21, inlined from 'static void phmap::priv::map_slot_policy::swap(Allocator*, slot_type*, slot_type*) [with Allocator = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; K = omnigraph::impl::EdgeId; V = omnigraph::de::NoLockingConstAdapter > >, phmap::Less, std::allocator > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:4554:56, inlined from 'static void phmap::priv::common_params::swap(Alloc*, slot_type*, slot_type*) [with Key = omnigraph::impl::EdgeId; Compare = phmap::Less; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; int TargetNodeSize = 256; bool Multi = false; SlotPolicy = phmap::priv::map_slot_policy > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/parallel_hashmap/btree.h:888:30, inlined from 'void phmap::priv::btree_node::swap(phmap::priv::btree_node*, allocator_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > > > >, phmap::Less, std::allocator > >, phmap::Less, std::allocator > > > > > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2382:30: /usr/include/c++/14/bits/new_allocator.h:172:33: warning: 'void operator delete(void*, std::size_t)' called on unallocated object 'empty_node' [-Wfree-nonheap-object] 172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:15: /usr/include/parallel_hashmap/btree.h: In function 'void phmap::priv::btree_node::swap(phmap::priv::btree_node*, allocator_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > > > >, phmap::Less, std::allocator > >, phmap::Less, std::allocator > > > > > > > >, 256, false>]': /usr/include/parallel_hashmap/btree.h:1623:44: note: declared here 1623 | static constexpr EmptyNodeType empty_node( | ^~~~~~~~~~ [ 92%] Linking CXX static library libstages.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/stages && /usr/bin/cmake -P CMakeFiles/stages.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/stages && /usr/bin/cmake -E cmake_link_script CMakeFiles/stages.dir/link.txt --verbose=1 /usr/bin/ar qc libstages.a CMakeFiles/stages.dir/read_conversion.cpp.o CMakeFiles/stages.dir/construction.cpp.o CMakeFiles/stages.dir/simplification.cpp.o CMakeFiles/stages.dir/ss_edge_split.cpp.o CMakeFiles/stages.dir/genomic_info_filler.cpp.o /usr/bin/ranlib libstages.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 92%] Built target stages make -f common/CMakeFiles/common_modules.dir/build.make common/CMakeFiles/common_modules.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/CMakeFiles/common_modules.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/CMakeFiles/common_modules.dir/build.make common/CMakeFiles/common_modules.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 92%] Building CXX object common/CMakeFiles/common_modules.dir/adt/concurrent_dsu.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/CMakeFiles/common_modules.dir/adt/concurrent_dsu.cpp.o -MF CMakeFiles/common_modules.dir/adt/concurrent_dsu.cpp.o.d -o CMakeFiles/common_modules.dir/adt/concurrent_dsu.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/concurrent_dsu.cpp [ 92%] Linking CXX static library libcommon_modules.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common && /usr/bin/cmake -P CMakeFiles/common_modules.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common && /usr/bin/cmake -E cmake_link_script CMakeFiles/common_modules.dir/link.txt --verbose=1 /usr/bin/ar qc libcommon_modules.a CMakeFiles/common_modules.dir/adt/concurrent_dsu.cpp.o /usr/bin/ranlib libcommon_modules.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 92%] Built target common_modules make -f projects/corrector/CMakeFiles/spades-corrector-core.dir/build.make projects/corrector/CMakeFiles/spades-corrector-core.dir/depend make -f projects/hammer/CMakeFiles/spades-hammer.dir/build.make projects/hammer/CMakeFiles/spades-hammer.dir/depend make -f projects/spades/CMakeFiles/spades-core.dir/build.make projects/spades/CMakeFiles/spades-core.dir/depend make -f projects/spades_tools/CMakeFiles/spades-convert-bin-to-fasta.dir/build.make projects/spades_tools/CMakeFiles/spades-convert-bin-to-fasta.dir/depend make -f projects/spades_tools/CMakeFiles/spades-gbuilder.dir/build.make projects/spades_tools/CMakeFiles/spades-gbuilder.dir/depend make -f projects/spades_tools/CMakeFiles/spades-gmapper.dir/build.make projects/spades_tools/CMakeFiles/spades-gmapper.dir/depend make -f projects/spades_tools/CMakeFiles/spades-gsimplifier.dir/build.make projects/spades_tools/CMakeFiles/spades-gsimplifier.dir/depend make -f projects/spades_tools/CMakeFiles/spades-kmercount.dir/build.make projects/spades_tools/CMakeFiles/spades-kmercount.dir/depend make -f projects/spades_tools/CMakeFiles/spades-read-filter.dir/build.make projects/spades_tools/CMakeFiles/spades-read-filter.dir/depend make -f projects/spades_tools/CMakeFiles/spades-kmer-estimating.dir/build.make projects/spades_tools/CMakeFiles/spades-kmer-estimating.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools/CMakeFiles/spades-kmercount.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools/CMakeFiles/spades-convert-bin-to-fasta.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades/CMakeFiles/spades-core.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools/CMakeFiles/spades-gsimplifier.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/corrector /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/corrector/CMakeFiles/spades-corrector-core.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools/CMakeFiles/spades-gbuilder.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools/CMakeFiles/spades-gmapper.dir/DependInfo.cmake "--color=" make -f projects/spades_tools/CMakeFiles/spades-gfa-split.dir/build.make projects/spades_tools/CMakeFiles/spades-gfa-split.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/hammer /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/hammer/CMakeFiles/spades-hammer.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools/CMakeFiles/spades-read-filter.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools/CMakeFiles/spades-kmer-estimating.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools/CMakeFiles/spades-gfa-split.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f projects/spades_tools/CMakeFiles/spades-kmercount.dir/build.make projects/spades_tools/CMakeFiles/spades-kmercount.dir/build make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f projects/spades/CMakeFiles/spades-core.dir/build.make projects/spades/CMakeFiles/spades-core.dir/build make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f projects/corrector/CMakeFiles/spades-corrector-core.dir/build.make projects/corrector/CMakeFiles/spades-corrector-core.dir/build make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f projects/hammer/CMakeFiles/spades-hammer.dir/build.make projects/hammer/CMakeFiles/spades-hammer.dir/build [ 92%] Building CXX object projects/spades_tools/CMakeFiles/spades-kmercount.dir/kmercount.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/spades_tools/CMakeFiles/spades-kmercount.dir/kmercount.cpp.o -MF CMakeFiles/spades-kmercount.dir/kmercount.cpp.o.d -o CMakeFiles/spades-kmercount.dir/kmercount.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f projects/spades_tools/CMakeFiles/spades-convert-bin-to-fasta.dir/build.make projects/spades_tools/CMakeFiles/spades-convert-bin-to-fasta.dir/build [ 93%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/pipeline.cpp.o [ 93%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/main.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/spades/CMakeFiles/spades-core.dir/main.cpp.o -MF CMakeFiles/spades-core.dir/main.cpp.o.d -o CMakeFiles/spades-core.dir/main.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/main.cpp make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 93%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o -MF CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector/positional_read.cpp make -f projects/spades_tools/CMakeFiles/spades-gbuilder.dir/build.make projects/spades_tools/CMakeFiles/spades-gbuilder.dir/build cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/spades/CMakeFiles/spades-core.dir/pipeline.cpp.o -MF CMakeFiles/spades-core.dir/pipeline.cpp.o.d -o CMakeFiles/spades-core.dir/pipeline.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/pipeline.cpp make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f projects/spades_tools/CMakeFiles/spades-gmapper.dir/build.make projects/spades_tools/CMakeFiles/spades-gmapper.dir/build [ 93%] Building CXX object projects/spades_tools/CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o [ 93%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/main.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/spades_tools/CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o -MF CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o.d -o CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/convert_bin_to_fasta.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=16777216UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/main.cpp.o -MF CMakeFiles/spades-hammer.dir/main.cpp.o.d -o CMakeFiles/spades-hammer.dir/main.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/main.cpp make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f projects/spades_tools/CMakeFiles/spades-gsimplifier.dir/build.make projects/spades_tools/CMakeFiles/spades-gsimplifier.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f projects/spades_tools/CMakeFiles/spades-read-filter.dir/build.make projects/spades_tools/CMakeFiles/spades-read-filter.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f projects/spades_tools/CMakeFiles/spades-kmer-estimating.dir/build.make projects/spades_tools/CMakeFiles/spades-kmer-estimating.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f projects/spades_tools/CMakeFiles/spades-gfa-split.dir/build.make projects/spades_tools/CMakeFiles/spades-gfa-split.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 95%] Building CXX object projects/spades_tools/CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/spades_tools/CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o -MF CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o.d -o CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmer_estimating.cpp [ 96%] Building CXX object projects/spades_tools/CMakeFiles/spades-gsimplifier.dir/__/cds_subgraphs/profile_storage.cpp.o [ 96%] Building CXX object projects/spades_tools/CMakeFiles/spades-gbuilder.dir/gbuilder.cpp.o [ 95%] Building CXX object projects/spades_tools/CMakeFiles/spades-gfa-split.dir/gfa_split.cpp.o [ 95%] Building CXX object projects/spades_tools/CMakeFiles/spades-gmapper.dir/gmapper.cpp.o [ 95%] Building CXX object projects/spades_tools/CMakeFiles/spades-read-filter.dir/read_filter.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/spades_tools/CMakeFiles/spades-gmapper.dir/gmapper.cpp.o -MF CMakeFiles/spades-gmapper.dir/gmapper.cpp.o.d -o CMakeFiles/spades-gmapper.dir/gmapper.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/gmapper.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/spades_tools/CMakeFiles/spades-gfa-split.dir/gfa_split.cpp.o -MF CMakeFiles/spades-gfa-split.dir/gfa_split.cpp.o.d -o CMakeFiles/spades-gfa-split.dir/gfa_split.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/gfa_split.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/spades_tools/CMakeFiles/spades-gsimplifier.dir/__/cds_subgraphs/profile_storage.cpp.o -MF CMakeFiles/spades-gsimplifier.dir/__/cds_subgraphs/profile_storage.cpp.o.d -o CMakeFiles/spades-gsimplifier.dir/__/cds_subgraphs/profile_storage.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/cds_subgraphs/profile_storage.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/spades_tools/CMakeFiles/spades-gbuilder.dir/gbuilder.cpp.o -MF CMakeFiles/spades-gbuilder.dir/gbuilder.cpp.o.d -o CMakeFiles/spades-gbuilder.dir/gbuilder.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/gbuilder.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/spades_tools/CMakeFiles/spades-read-filter.dir/read_filter.cpp.o -MF CMakeFiles/spades-read-filter.dir/read_filter.cpp.o.d -o CMakeFiles/spades-read-filter.dir/read_filter.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/read_filter.cpp [ 97%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o -MF CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector/interesting_pos_processor.cpp /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/pipeline.cpp: In function 'void spades::AddPreliminarySimplificationStages(StageManager&)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/pipeline.cpp:134:19: warning: unused variable 'mode' [-Wunused-variable] 134 | pipeline_type mode = cfg::get().mode; | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/pipeline.cpp: In function 'void spades::assemble_genome()': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/pipeline.cpp:236:46: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'unsigned int' may change value [-Wconversion] 236 | graph_pack::GraphPack conj_gp(cfg::get().K, | ~~~~~~~~~~~^ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/gbuilder.cpp:25: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:30:10: required from here 30 | bool Load(const std::string &basename, Graph &graph) override { | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:31:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 31 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:43:10: required from here 43 | bool BinRead(std::istream &is, Graph &graph) override { | ^~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:44:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 44 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:10: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:47:10: required from here 47 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:61:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 61 | auto new_id = graph.AddVertex(typename Graph::VertexData(graph.k()), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:83:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 83 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/gmapper.cpp:25: /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp: In function 'std::string debruijn_graph::gap_closing::SPOAConsensus(const std::vector >&, const debruijn_graph::config::pacbio_processor&)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp:329:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 329 | while (pref_remove < coverages.size() && coverages[pref_remove] < cov / 2 ) | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp: In member function 'void debruijn_graph::gap_closing::MultiGapJoiner::UpdateGap(debruijn_graph::gap_closing::GapDescription&, debruijn_graph::gap_closing::EdgePair, debruijn_graph::gap_closing::EdgePair) const': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp:485:14: warning: unused variable 'u1' [-Wunused-variable] 485 | bool u1 = UpdateLeft(gap, split_orig, split_res); | ^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp:486:14: warning: unused variable 'u2' [-Wunused-variable] 486 | bool u2 = UpdateRight(gap, split_orig, split_res); | ^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp: In member function 'debruijn_graph::gap_closing::GapDescription debruijn_graph::gap_closing::HybridGapCloser::ConstructConsensus(gap_info_it, gap_info_it) const': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp:659:16: warning: unused variable 'cur_len' [-Wunused-variable] 659 | size_t cur_len = end_it - start_it; | ^~~~~~~ [ 97%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o -MF CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector/contig_processor.cpp [ 97%] Building CXX object projects/spades_tools/CMakeFiles/spades-gsimplifier.dir/gsimplifier.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/spades_tools/CMakeFiles/spades-gsimplifier.dir/gsimplifier.cpp.o -MF CMakeFiles/spades-gsimplifier.dir/gsimplifier.cpp.o.d -o CMakeFiles/spades-gsimplifier.dir/gsimplifier.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/gsimplifier.cpp /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector/contig_processor.cpp: In member function 'bool corrector::ContigProcessor::CountPositions(const sam_reader::SingleSamRead&, std::unordered_map&) const': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector/contig_processor.cpp:162:65: warning: conversion from 'std::size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 162 | if ((aligned_length < min(read_len_double * 0.4, 40.0)) && (position > read_len_double / 2) && (contig_.length() > read_len_double / 2 + (double) position)) { | ^~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector/contig_processor.cpp:162:115: warning: conversion from 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 162 | if ((aligned_length < min(read_len_double * 0.4, 40.0)) && (position > read_len_double / 2) && (contig_.length() > read_len_double / 2 + (double) position)) { | ~~~~~~~~~~~~~~^~ [ 97%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/series_analysis.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/spades/CMakeFiles/spades-core.dir/series_analysis.cpp.o -MF CMakeFiles/spades-core.dir/series_analysis.cpp.o.d -o CMakeFiles/spades-core.dir/series_analysis.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/series_analysis.cpp In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:36, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/sequence.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/reads/single_read.hpp:13, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/reads/io_helper.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp:14: In function 'xxh_u64 XXH_read64(const void*)', inlined from 'xxh_u64 XXH_readLE64(const void*)' at /usr/include/xxhash.h:3425:34, inlined from 'xxh_u64 XXH3_mix16B(const xxh_u8*, const xxh_u8*, xxh_u64)' at /usr/include/xxhash.h:4755:46, inlined from 'XXH64_hash_t XXH3_len_17to128_64b(const xxh_u8*, size_t, const xxh_u8*, size_t, XXH64_hash_t)' at /usr/include/xxhash.h:4785:39, inlined from 'XXH64_hash_t XXH3_64bits_internal(const void*, size_t, XXH64_hash_t, const void*, size_t, XXH3_hashLong64_f)' at /usr/include/xxhash.h:6175:36, inlined from 'XXH64_hash_t XXH_INLINE_XXH3_64bits_withSeed(const void*, size_t, XXH64_hash_t)' at /usr/include/xxhash.h:6201:32, inlined from 'static size_t RuntimeSeq::GetHash(const DataType*, size_t, uint64_t) [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:691:36, inlined from 'size_t RuntimeSeq::GetHash(uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:695:23, inlined from 'size_t RuntimeSeq::hash::operator()(const RuntimeSeq&, uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:700:31, inlined from 'size_t kmer::KMerSegmentPolicy::operator()(const Seq&) const [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/kmer_mph/kmer_buckets.hpp:51:22, inlined from 'bool kmers::KMerSortingSplitter::push_back_internal(const Seq&, unsigned int) [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/kmer_mph/kmer_splitter.hpp:116:35, inlined from 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)' at /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp:79:51: /usr/include/xxhash.h:3356:39: warning: array subscript 6 is outside array bounds of 'RtSeq [1]' {aka 'RuntimeSeq<128> [1]'} [-Warray-bounds=] 3356 | return *((const xxh_unalign64*)ptr); | ^ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp: In member function 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp:76:17: note: at offset 48 into object 'kmer' of size 40 76 | RtSeq kmer = seq.start(this->K_) >> 'A'; | ^~~~ In function 'xxh_u64 XXH_read64(const void*)', inlined from 'xxh_u64 XXH_readLE64(const void*)' at /usr/include/xxhash.h:3425:34, inlined from 'xxh_u64 XXH3_mix16B(const xxh_u8*, const xxh_u8*, xxh_u64)' at /usr/include/xxhash.h:4756:46, inlined from 'XXH64_hash_t XXH3_len_17to128_64b(const xxh_u8*, size_t, const xxh_u8*, size_t, XXH64_hash_t)' at /usr/include/xxhash.h:4785:39, inlined from 'XXH64_hash_t XXH3_64bits_internal(const void*, size_t, XXH64_hash_t, const void*, size_t, XXH3_hashLong64_f)' at /usr/include/xxhash.h:6175:36, inlined from 'XXH64_hash_t XXH_INLINE_XXH3_64bits_withSeed(const void*, size_t, XXH64_hash_t)' at /usr/include/xxhash.h:6201:32, inlined from 'static size_t RuntimeSeq::GetHash(const DataType*, size_t, uint64_t) [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:691:36, inlined from 'size_t RuntimeSeq::GetHash(uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:695:23, inlined from 'size_t RuntimeSeq::hash::operator()(const RuntimeSeq&, uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:700:31, inlined from 'size_t kmer::KMerSegmentPolicy::operator()(const Seq&) const [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/kmer_mph/kmer_buckets.hpp:51:22, inlined from 'bool kmers::KMerSortingSplitter::push_back_internal(const Seq&, unsigned int) [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/kmer_mph/kmer_splitter.hpp:116:35, inlined from 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)' at /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp:79:51: /usr/include/xxhash.h:3356:39: warning: array subscript 7 is outside array bounds of 'RtSeq [1]' {aka 'RuntimeSeq<128> [1]'} [-Warray-bounds=] 3356 | return *((const xxh_unalign64*)ptr); | ^ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp: In member function 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp:76:17: note: at offset 56 into object 'kmer' of size 40 76 | RtSeq kmer = seq.start(this->K_) >> 'A'; | ^~~~ In function 'xxh_u64 XXH_read64(const void*)', inlined from 'xxh_u64 XXH_readLE64(const void*)' at /usr/include/xxhash.h:3425:34, inlined from 'xxh_u64 XXH3_mix16B(const xxh_u8*, const xxh_u8*, xxh_u64)' at /usr/include/xxhash.h:4755:46, inlined from 'XXH64_hash_t XXH3_len_17to128_64b(const xxh_u8*, size_t, const xxh_u8*, size_t, XXH64_hash_t)' at /usr/include/xxhash.h:4786:39, inlined from 'XXH64_hash_t XXH3_64bits_internal(const void*, size_t, XXH64_hash_t, const void*, size_t, XXH3_hashLong64_f)' at /usr/include/xxhash.h:6175:36, inlined from 'XXH64_hash_t XXH_INLINE_XXH3_64bits_withSeed(const void*, size_t, XXH64_hash_t)' at /usr/include/xxhash.h:6201:32, inlined from 'static size_t RuntimeSeq::GetHash(const DataType*, size_t, uint64_t) [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:691:36, inlined from 'size_t RuntimeSeq::GetHash(uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:695:23, inlined from 'size_t RuntimeSeq::hash::operator()(const RuntimeSeq&, uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:700:31, inlined from 'size_t kmer::KMerSegmentPolicy::operator()(const Seq&) const [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/kmer_mph/kmer_buckets.hpp:51:22, inlined from 'bool kmers::KMerSortingSplitter::push_back_internal(const Seq&, unsigned int) [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/kmer_mph/kmer_splitter.hpp:116:35, inlined from 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)' at /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp:79:51: /usr/include/xxhash.h:3356:39: warning: array subscript 'const xxh_unalign64 {aka const long unsigned int}[4]' is partly outside array bounds of 'RtSeq [1]' {aka 'RuntimeSeq<128> [1]'} [-Warray-bounds=] 3356 | return *((const xxh_unalign64*)ptr); | ^ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp: In member function 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp:76:17: note: at offset [33, 40] into object 'kmer' of size 40 76 | RtSeq kmer = seq.start(this->K_) >> 'A'; | ^~~~ In function 'xxh_u64 XXH_read64(const void*)', inlined from 'xxh_u64 XXH_readLE64(const void*)' at /usr/include/xxhash.h:3425:34, inlined from 'xxh_u64 XXH3_mix16B(const xxh_u8*, const xxh_u8*, xxh_u64)' at /usr/include/xxhash.h:4756:46, inlined from 'XXH64_hash_t XXH3_len_17to128_64b(const xxh_u8*, size_t, const xxh_u8*, size_t, XXH64_hash_t)' at /usr/include/xxhash.h:4786:39, inlined from 'XXH64_hash_t XXH3_64bits_internal(const void*, size_t, XXH64_hash_t, const void*, size_t, XXH3_hashLong64_f)' at /usr/include/xxhash.h:6175:36, inlined from 'XXH64_hash_t XXH_INLINE_XXH3_64bits_withSeed(const void*, size_t, XXH64_hash_t)' at /usr/include/xxhash.h:6201:32, inlined from 'static size_t RuntimeSeq::GetHash(const DataType*, size_t, uint64_t) [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:691:36, inlined from 'size_t RuntimeSeq::GetHash(uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:695:23, inlined from 'size_t RuntimeSeq::hash::operator()(const RuntimeSeq&, uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:700:31, inlined from 'size_t kmer::KMerSegmentPolicy::operator()(const Seq&) const [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/kmer_mph/kmer_buckets.hpp:51:22, inlined from 'bool kmers::KMerSortingSplitter::push_back_internal(const Seq&, unsigned int) [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/kmer_mph/kmer_splitter.hpp:116:35, inlined from 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)' at /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp:79:51: /usr/include/xxhash.h:3356:39: warning: array subscript [5, 6] is outside array bounds of 'RtSeq [1]' {aka 'RuntimeSeq<128> [1]'} [-Warray-bounds=] 3356 | return *((const xxh_unalign64*)ptr); | ^ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp: In member function 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp:76:17: note: at offset [41, 48] into object 'kmer' of size 40 76 | RtSeq kmer = seq.start(this->K_) >> 'A'; | ^~~~ In function 'xxh_u64 XXH_read64(const void*)', inlined from 'xxh_u64 XXH_readLE64(const void*)' at /usr/include/xxhash.h:3425:34, inlined from 'xxh_u64 XXH3_mix16B(const xxh_u8*, const xxh_u8*, xxh_u64)' at /usr/include/xxhash.h:4756:46, inlined from 'XXH64_hash_t XXH3_len_17to128_64b(const xxh_u8*, size_t, const xxh_u8*, size_t, XXH64_hash_t)' at /usr/include/xxhash.h:4788:35, inlined from 'XXH64_hash_t XXH3_64bits_internal(const void*, size_t, XXH64_hash_t, const void*, size_t, XXH3_hashLong64_f)' at /usr/include/xxhash.h:6175:36, inlined from 'XXH64_hash_t XXH_INLINE_XXH3_64bits_withSeed(const void*, size_t, XXH64_hash_t)' at /usr/include/xxhash.h:6201:32, inlined from 'static size_t RuntimeSeq::GetHash(const DataType*, size_t, uint64_t) [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:691:36, inlined from 'size_t RuntimeSeq::GetHash(uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:695:23, inlined from 'size_t RuntimeSeq::hash::operator()(const RuntimeSeq&, uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:700:31, inlined from 'size_t kmer::KMerSegmentPolicy::operator()(const Seq&) const [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/kmer_mph/kmer_buckets.hpp:51:22, inlined from 'bool kmers::KMerSortingSplitter::push_back_internal(const Seq&, unsigned int) [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/kmer_mph/kmer_splitter.hpp:116:35, inlined from 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)' at /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp:79:51: /usr/include/xxhash.h:3356:39: warning: array subscript 5 is outside array bounds of 'RtSeq [1]' {aka 'RuntimeSeq<128> [1]'} [-Warray-bounds=] 3356 | return *((const xxh_unalign64*)ptr); | ^ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp: In member function 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp:76:17: note: at offset 40 into object 'kmer' of size 40 76 | RtSeq kmer = seq.start(this->K_) >> 'A'; | ^~~~ [ 97%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=16777216UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o -MF CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o.d -o CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/hammer_tools.cpp [ 97%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/spades/CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o -MF CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o.d -o CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/mts/contig_abundance.cpp In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/observable_graph.hpp:13, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/bwa_index.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/gmapper.cpp:8: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 508 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/parallel_processing.hpp:378:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity; size_t = long unsigned int]' 378 | for (; !it_.IsEnd(); ++it_) { | ^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/compressor.hpp:130:26: required from 'size_t omnigraph::CompressAllVertices(Graph&, size_t, bool) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 130 | return compressor.Run(); | ~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp:752:28: required from here 752 | CompressAllVertices(g_, /*chunk_cnt*/100); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/gmapper.cpp:19: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:47:10: required from here 47 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:61:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 61 | auto new_id = graph.AddVertex(typename Graph::VertexData(graph.k()), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:83:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 83 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/gsimplifier.cpp:8: /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/simplification.hpp: In function 'void debruijn::simplification::Simplify(graph_pack::GraphPack&, const SimplifInfoContainer&, bool, const std::function&)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/simplification.hpp:103:16: warning: unused variable 'using_edge_qual' [-Wunused-variable] 103 | const bool using_edge_qual = edge_qual.IsAttached(); | ^~~~~~~~~~~~~~~ [ 97%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o -MF CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector/dataset_processor.cpp In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/chimera_stats.hpp:13, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/graph_simplification.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/simplification.hpp:9: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp: In instantiation of 'void omnigraph::simplification::relative_coverage::Component::RemoveFromBorder(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp:85:9: required from 'void omnigraph::simplification::relative_coverage::Component::MakeInner(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' 85 | RemoveFromBorder(v); | ^~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp:506:37: required from 'bool omnigraph::simplification::relative_coverage::component_remover::InnerComponentSearcher::FindComponent() [with Graph = debruijn_graph::DeBruijnGraph]' 506 | component_.MakeInner(v); | ~~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp:669:49: required from 'std::optional > omnigraph::simplification::relative_coverage::component_remover::RelativeCovComponentFinder::operator()(EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]' 669 | if (component_searcher.FindComponent()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp:722:61: required from 'omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover::RelativeCoverageComponentRemover(Graph&, size_t, const omnigraph::FlankingCoverage&, double, size_t, size_t, size_t, double, HandlerF, size_t, std::filesystem::__cxx11::path) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int; HandlerF = std::function, std::allocator >&)>]' 722 | [&](EdgeId e) { return static_cast(finder_(e)); }, chunk_cnt); | ~~~~~~~^~~ /usr/include/c++/14/bits/stl_construct.h:119:7: required from 'constexpr void std::_Construct(_Tp*, _Args&& ...) [with _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, function, allocator >&)>&, const long unsigned int&, filesystem::__cxx11::path&}]' 119 | ::new((void*)__p) _Tp(std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/alloc_traits.h:706:19: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /usr/include/c++/14/bits/shared_ptr_base.h:969:16: required from 'std::__shared_count<_Lp>::__shared_count(_Tp*&, std::_Sp_alloc_shared_tag<_Alloc>, _Args&& ...) [with _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; _Alloc = std::allocator; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::filesystem::__cxx11::path&}; __gnu_cxx::_Lock_policy _Lp = __gnu_cxx::_S_atomic]' 969 | auto __pi = ::new (__mem) | ^~~~~~~~~~~~~ 970 | _Sp_cp_type(__a._M_a, std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/shared_ptr_base.h:1713:14: required from 'std::__shared_ptr<_Tp, _Lp>::__shared_ptr(std::_Sp_alloc_shared_tag<_Tp>, _Args&& ...) [with _Alloc = std::allocator; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::filesystem::__cxx11::path&}; _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; __gnu_cxx::_Lock_policy _Lp = __gnu_cxx::_S_atomic]' 1713 | : _M_ptr(), _M_refcount(_M_ptr, __tag, std::forward<_Args>(__args)...) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/shared_ptr.h:463:59: required from 'std::shared_ptr<_Tp>::shared_ptr(std::_Sp_alloc_shared_tag<_Tp>, _Args&& ...) [with _Alloc = std::allocator; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::filesystem::__cxx11::path&}; _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover]' 463 | : __shared_ptr<_Tp>(__tag, std::forward<_Args>(__args)...) | ^ /usr/include/c++/14/bits/shared_ptr.h:1007:14: required from 'std::shared_ptr > std::make_shared(_Args&& ...) [with _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, function, allocator >&)>&, const long unsigned int&, filesystem::__cxx11::path&}; _NonArray<_Tp> = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover]' 1007 | return shared_ptr<_Tp>(_Sp_alloc_shared_tag<_Alloc>{__a}, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1008 | std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/graph_simplification.hpp:438:49: required from 'omnigraph::AlgoPtr debruijn::simplification::RelativeCoverageComponentRemoverInstance(Graph&, const omnigraph::FlankingCoverage&, const debruijn_graph::config::debruijn_config::simplification::relative_coverage_comp_remover&, const SimplifInfoContainer&, typename omnigraph::ComponentRemover::HandlerF) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::AlgoPtr = std::shared_ptr >; typename omnigraph::ComponentRemover::HandlerF = std::function, std::allocator >&)>]' 437 | return std::make_shared>(g, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 439 | info.chunk_cnt(), | ~~~~~~~~~~~~~~~~~ 440 | flanking_cov, | ~~~~~~~~~~~~~ 441 | rcc_config.coverage_gap, | ~~~~~~~~~~~~~~~~~~~~~~~~ 442 | size_t(double(info.read_length()) * rcc_config.length_coeff), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 443 | size_t(double(info.read_length()) * rcc_config.tip_allowing_length_coeff), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 444 | connecting_path_length_bound, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 445 | max_coverage, | ~~~~~~~~~~~~~ 446 | removal_handler, rcc_config.vertex_count_limit, pics_dir); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/simplification.hpp:157:65: required from here 157 | algo.AddAlgo(RelativeCoverageComponentRemoverInstance(graph, flanking_cov, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 158 | rcc_config(rel_cov_proc_enabled), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 159 | simplif_info, set_removal_handler_f), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp:55:16: warning: unused variable 'cnt' [-Wunused-variable] 55 | size_t cnt = border_.erase(v); | ^~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/gsimplifier.cpp:13: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:30:10: required from here 30 | bool Load(const std::string &basename, Graph &graph) override { | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:31:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 31 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:43:10: required from here 43 | bool BinRead(std::istream &is, Graph &graph) override { | ^~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:44:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 44 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:10: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:47:10: required from here 47 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:61:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 61 | auto new_id = graph.AddVertex(typename Graph::VertexData(graph.k()), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:83:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 83 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/graph_simplification.hpp:19: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/bulge_remover.hpp: In instantiation of 'omnigraph::ParallelBulgeRemover::SmartEdgeSet omnigraph::ParallelBulgeRemover::RetainIndependentBulges(std::vector&) const [with Graph = debruijn_graph::DeBruijnGraph; SmartEdgeSet = omnigraph::SmartSetIterator >]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/bulge_remover.hpp:721:42: required from 'size_t omnigraph::ParallelBulgeRemover::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 721 | auto interacting_edges = RetainIndependentBulges(bulges); | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/bulge_remover.hpp:678:12: required from here 678 | size_t Run(bool force_primary_launch, double /*iter_run_progress*/) override { | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/bulge_remover.hpp:582:16: warning: unused variable 'total_cnt' [-Wunused-variable] 582 | size_t total_cnt = bulges.size(); | ^~~~~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/observable_graph.hpp:13, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/graph_simplification.hpp:11: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap >]' 508 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/parallel_processing.hpp:378:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator; size_t = long unsigned int]' 378 | for (; !it_.IsEnd(); ++it_) { | ^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/parallel_processing.hpp:354:12: required from here 354 | size_t Run(bool force_primary_launch = false, | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 508 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/parallel_processing.hpp:378:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity; size_t = long unsigned int]' 378 | for (; !it_.IsEnd(); ++it_) { | ^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/parallel_processing.hpp:354:12: required from here 354 | size_t Run(bool force_primary_launch = false, | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap >]' 508 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/parallel_processing.hpp:378:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator; size_t = long unsigned int]' 378 | for (; !it_.IsEnd(); ++it_) { | ^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/parallel_processing.hpp:354:12: required from here 354 | size_t Run(bool force_primary_launch = false, | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ [ 97%] Linking CXX executable ../../bin/spades-convert-bin-to-fasta cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-convert-bin-to-fasta.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/spades-convert-bin-to-fasta.dir/link.d "CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-convert-bin-to-fasta ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/kmer_index/libmph_index.a ../../common/modules/libmodules.a ../../common/configs/libconfigs.a ../../common/library/liblibrary.a ../../common/io/libinput.a ../../common/io/sam/libsamio.a ../../ext/samtools/libsamtools.a /usr/lib/x86_64-linux-gnu/libbamtools.so ../../common/io/binary/libbinary_io.a ../../common/alignment/libalignment.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/bwa/libbwa.a ../../_deps/zlib_ng-build/libz.a -lm make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 97%] Built target spades-convert-bin-to-fasta [ 97%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o -MF CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector/config_struct.cpp [ 97%] Linking CXX executable ../../bin/spades-kmer-estimating cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-kmer-estimating.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/spades-kmer-estimating.dir/link.d "CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-kmer-estimating ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/kmer_index/libmph_index.a ../../common/modules/libmodules.a ../../common/configs/libconfigs.a ../../common/library/liblibrary.a ../../common/io/libinput.a ../../common/io/sam/libsamio.a ../../ext/samtools/libsamtools.a /usr/lib/x86_64-linux-gnu/libbamtools.so ../../common/io/binary/libbinary_io.a ../../common/alignment/libalignment.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/bwa/libbwa.a ../../_deps/zlib_ng-build/libz.a -lm make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 97%] Built target spades-kmer-estimating [ 97%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/main.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/main.cpp.o -MF CMakeFiles/spades-corrector-core.dir/main.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/main.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector/main.cpp [ 97%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/hamcluster.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=16777216UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/hamcluster.cpp.o -MF CMakeFiles/spades-hammer.dir/hamcluster.cpp.o.d -o CMakeFiles/spades-hammer.dir/hamcluster.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/hamcluster.cpp [ 98%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=16777216UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o -MF CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o.d -o CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/kmer_cluster.cpp [ 98%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/kmer_data.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=16777216UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/kmer_data.cpp.o -MF CMakeFiles/spades-hammer.dir/kmer_data.cpp.o.d -o CMakeFiles/spades-hammer.dir/kmer_data.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/kmer_data.cpp [ 98%] Linking CXX executable ../../bin/spades-core cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-core.dir/link.txt --verbose=1 [ 98%] Linking CXX executable ../../bin/spades-read-filter cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-read-filter.dir/link.txt --verbose=1 In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/hamcluster.cpp:13: /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/parallel_radix_sort.hpp: In instantiation of 'void parallel_radix_sort::value_manager::PairValueManager::Start(ValueType*, size_t, int) [with ValueType = long unsigned int; int Base = 8; size_t = long unsigned int]': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/parallel_radix_sort.hpp:544:13: required from 'static void parallel_radix_sort::PairSort::InitAndSort(PlainType*, ValueType*, size_t, int) [with PlainType = Seq<11, unsigned int>; ValueType = long unsigned int; UnsignedType = Seq<11, unsigned int>; Encoder = EncoderKMer; int Base = 8; size_t = long unsigned int]' 544 | vm.Start(vals, num_elems, num_threads); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/hamcluster.cpp:55:26: required from 'std::pair SubKMerSplitter::split(Op&&) [with Op = KMerHamClusterer::cluster(const std::string&, const KMerData&, dsu::ConcurrentDSU&)::::iterator&, size_t)>]' 55 | PairSort::InitAndSort(data.data(), blocks.data(), data.size(), data.size() > 1000*16 ? -1 : 1); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/hamcluster.cpp:148:21: required from here 148 | Splitter.split([&] (const std::vector::iterator &start, size_t sz) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 149 | if (sz < block_thr) { | ~~~~~~~~~~~~~~~~~~~~~ 150 | // Merge small blocks. | ~~~~~~~~~~~~~~~~~~~~~~ 151 | processBlockQuadratic(uf, start, sz, data, tau_); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 152 | } else { | ~~~~~~~~ 153 | big_blocks1 += 1; | ~~~~~~~~~~~~~~~~~ 154 | // Otherwise - dump for next iteration. | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 155 | for (unsigned i = 0; i < tau_ + 1; ++i) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 156 | serialize(bfs, kfs, | ~~~~~~~~~~~~~~~~~~~ 157 | data, &start, sz, | ~~~~~~~~~~~~~~~~~ 158 | SubKMerStridedSerializer(i, tau_ + 1)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 159 | } | ~ 160 | } | ~ 161 | }); | ~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/parallel_radix_sort.hpp:401:42: warning: unused parameter 'num_elems' [-Wunused-parameter] 401 | void Start(ValueType *original, size_t num_elems, int num_threads) { | ~~~~~~~^~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/parallel_radix_sort.hpp:401:57: warning: unused parameter 'num_threads' [-Wunused-parameter] 401 | void Start(ValueType *original, size_t num_elems, int num_threads) { | ~~~~^~~~~~~~~~~ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/spades-read-filter.dir/link.d "CMakeFiles/spades-read-filter.dir/read_filter.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-read-filter ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/kmer_index/libmph_index.a ../../common/modules/libmodules.a ../../common/configs/libconfigs.a ../../common/library/liblibrary.a ../../common/io/libinput.a ../../common/io/sam/libsamio.a ../../ext/samtools/libsamtools.a /usr/lib/x86_64-linux-gnu/libbamtools.so ../../common/io/binary/libbinary_io.a ../../common/alignment/libalignment.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/bwa/libbwa.a ../../_deps/zlib_ng-build/libz.a -lm make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 98%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=16777216UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o -MF CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o.d -o CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/config_struct_hammer.cpp [ 98%] Built target spades-read-filter [ 98%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/read_corrector.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=16777216UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/read_corrector.cpp.o -MF CMakeFiles/spades-hammer.dir/read_corrector.cpp.o.d -o CMakeFiles/spades-hammer.dir/read_corrector.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/read_corrector.cpp [ 98%] Linking CXX executable ../../bin/spades-gfa-split cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-gfa-split.dir/link.txt --verbose=1 [ 98%] Linking CXX executable ../../bin/spades-corrector-core cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-corrector-core.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/spades-gfa-split.dir/link.d "CMakeFiles/spades-gfa-split.dir/gfa_split.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-gfa-split ../../common/io/graph/libgraphio.a ../../common/toolchain/libtoolchain.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/io/graph/libgraphio.a ../../ext/lexy/src/liblexy_file.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/kmer_index/libmph_index.a ../../common/modules/libmodules.a ../../common/configs/libconfigs.a ../../common/library/liblibrary.a ../../common/io/libinput.a ../../common/io/binary/libbinary_io.a ../../common/io/sam/libsamio.a ../../ext/samtools/libsamtools.a /usr/lib/x86_64-linux-gnu/libbamtools.so ../../common/alignment/libalignment.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/bwa/libbwa.a ../../_deps/zlib_ng-build/libz.a -lm make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 98%] Built target spades-gfa-split [ 98%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/expander.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=16777216UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/expander.cpp.o -MF CMakeFiles/spades-hammer.dir/expander.cpp.o.d -o CMakeFiles/spades-hammer.dir/expander.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/expander.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/spades-corrector-core.dir/link.d "CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o" "CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o" "CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o" "CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o" "CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o" "CMakeFiles/spades-corrector-core.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-corrector-core ../../common/io/libinput.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/kmer_index/libmph_index.a ../../common/modules/libmodules.a ../../common/configs/libconfigs.a ../../common/library/liblibrary.a ../../common/io/libinput.a ../../common/io/sam/libsamio.a ../../ext/samtools/libsamtools.a /usr/lib/x86_64-linux-gnu/libbamtools.so ../../common/io/binary/libbinary_io.a ../../common/alignment/libalignment.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/bwa/libbwa.a ../../_deps/zlib_ng-build/libz.a -lm make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 98%] Built target spades-corrector-core /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/read_corrector.cpp: In member function 'std::string ReadCorrector::CorrectReadRight(const std::string&, const std::string&, size_t)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/read_corrector.cpp:73:57: warning: conversion from 'long unsigned int' to 'double' may change value [-Wconversion] 73 | const size_t size_thr = size_t(100 * log2(read_size - right_pos)) + 1; | ~~~~~~~~~~^~~~~~~~~~~ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/spades-core.dir/link.d "CMakeFiles/spades-core.dir/pipeline.cpp.o" "CMakeFiles/spades-core.dir/main.cpp.o" "CMakeFiles/spades-core.dir/series_analysis.cpp.o" "CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-core libspades-stages.a ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/hmm/libhmmercpp.a ../../ext/hmmer/libhmmer.a -lspoa ../../ext/easel/libeasel.a ../../ext/lexy/src/liblexy_file.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/kmer_index/libmph_index.a ../../common/modules/libmodules.a ../../common/configs/libconfigs.a ../../common/library/liblibrary.a ../../common/io/libinput.a ../../common/io/sam/libsamio.a ../../ext/samtools/libsamtools.a /usr/lib/x86_64-linux-gnu/libbamtools.so ../../common/io/binary/libbinary_io.a ../../common/alignment/libalignment.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/bwa/libbwa.a ../../_deps/zlib_ng-build/libz.a -lm make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 98%] Built target spades-core [100%] Linking CXX executable ../../bin/spades-kmercount cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-kmercount.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/spades-kmercount.dir/link.d "CMakeFiles/spades-kmercount.dir/kmercount.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-kmercount ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/kmer_index/libmph_index.a ../../common/modules/libmodules.a ../../common/configs/libconfigs.a ../../common/library/liblibrary.a ../../common/io/libinput.a ../../common/io/sam/libsamio.a ../../ext/samtools/libsamtools.a /usr/lib/x86_64-linux-gnu/libbamtools.so ../../common/io/binary/libbinary_io.a ../../common/alignment/libalignment.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/bwa/libbwa.a ../../_deps/zlib_ng-build/libz.a -lm make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [100%] Built target spades-kmercount /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/kmer_cluster.cpp: In member function 'size_t KMerClustering::SubClusterSingle(const std::vector&, std::vector >&)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/kmer_cluster.cpp:344:9: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 344 | for (uint32_t j=0; j&)': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graphio.cpp:192:13: warning: variable 'read_count' set but not used [-Wunused-but-set-variable] 192 | int read_count = fscanf(file, "%zu\n", &pos_count); | ^~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/io_test.cpp: In function 'void CheckGFAInOut(const std::string&, const std::string&, const std::filesystem::__cxx11::path&)': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/io_test.cpp:63:17: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'unsigned int' may change value [-Wconversion] 63 | Graph graph(K); | ^ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/io_test.cpp:73:21: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'unsigned int' may change value [-Wconversion] 73 | Graph gfa_graph(K); | ^ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/construction_test.cpp: In function 'void CheckIndex(const std::vector >&, const std::filesystem::__cxx11::path&, size_t)': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/construction_test.cpp:68:30: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'unsigned int' may change value [-Wconversion] 68 | graph_pack::GraphPack gp(k, tmpdir, 0); | ^ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/observable_graph.hpp:13, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/random_graph.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/io_test.cpp:10: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 508 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/io_test.cpp:51:38: required from here 51 | for (size_t i = 0; i < 5; ++i, ++it) | ^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ [ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/test.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/test.cpp.o -MF CMakeFiles/debruijn_test.dir/test.cpp.o.d -o CMakeFiles/debruijn_test.dir/test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/test.cpp /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 508 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/io_test.cpp:38:9: required from 'void CompareGraphIterators(I, I) [with I = omnigraph::SmartEdgeIterator, adt::identity>]' 38 | ++it1; | ^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/io_test.cpp:95:26: required from here 95 | CompareGraphIterators(graph.SmartEdgeBegin(), new_graph.SmartEdgeBegin()); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/test_utils.cpp: In function 'void test_utils::AssertGraph(size_t, const std::vector >&, const std::vector >&)': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/test_utils.cpp:131:13: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'unsigned int' may change value [-Wconversion] 131 | Graph g(k); | ^ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/test_utils.cpp: In function 'void test_utils::AssertGraph(size_t, const std::vector, std::__cxx11::basic_string > >&, size_t, size_t, const std::vector >&, const CoverageInfo&, const EdgePairInfo&)': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/test_utils.cpp:193:30: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'unsigned int' may change value [-Wconversion] 193 | graph_pack::GraphPack gp(k, "tmp", 1); | ^ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/observable_graph.hpp:13, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/random_graph.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/paired_info_test.cpp:8: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 508 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/random_graph.hpp:49:62: required from 'debruijn_graph::RandomGraphAccessor::EdgeId debruijn_graph::RandomGraphAccessor::GetRandomEdge() const [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]' 49 | for (auto it = graph_.SmartEdgeBegin(); !it.IsEnd(); ++it) { | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/random_graph.hpp:174:48: required from 'void debruijn_graph::RandomPairedIndex::RemoveRandomEdgeInfo() [with Index = omnigraph::de::PairedIndex]' 174 | this->value_.Remove(this->GetRandomEdge()); | ~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/random_graph.hpp:185:13: required from 'void debruijn_graph::RandomPairedIndex::PerformRandomOperation() [with Index = omnigraph::de::PairedIndex]' 185 | RemoveRandomEdgeInfo(); | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/random_graph.hpp:177:10: required from here 177 | void PerformRandomOperation() override { | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 508 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/random_graph.hpp:41:13: required from 'debruijn_graph::RandomGraphAccessor::VertexId debruijn_graph::RandomGraphAccessor::GetRandomVertex() const [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' 41 | ++it; | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/random_graph.hpp:101:51: required from 'void debruijn_graph::RandomGraph::AddRandomEdge() [with Graph = debruijn_graph::DeBruijnGraph]' 101 | this->value_.AddEdge(this->GetRandomVertex(), this->GetRandomVertex(), | ~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/random_graph.hpp:120:17: required from 'void debruijn_graph::RandomGraph::PerformRandomOperation() [with Graph = debruijn_graph::DeBruijnGraph]' 120 | AddRandomEdge(); | ^~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/random_graph.hpp:113:10: required from here 113 | void PerformRandomOperation() override { | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/io_test.cpp:12: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:47:10: required from here 47 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:61:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 61 | auto new_id = graph.AddVertex(typename Graph::VertexData(graph.k()), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:83:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 83 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/random_graph.hpp:11: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/kmer_mapper.hpp: In instantiation of 'void debruijn_graph::KmerMapper::HandleGlue(EdgeId, EdgeId, EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/kmer_mapper.hpp:148:10: required from here 148 | void HandleGlue(EdgeId new_edge, EdgeId edge1, EdgeId edge2) override { | ^~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/kmer_mapper.hpp:148:28: warning: unused parameter 'new_edge' [-Wunused-parameter] 148 | void HandleGlue(EdgeId new_edge, EdgeId edge1, EdgeId edge2) override { | ~~~~~~~^~~~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/v_overlaps.cpp:8: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/construction_helper.hpp: In instantiation of 'void omnigraph::ConstructionHelper::DeleteLink(VertexId, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster; VertexId = omnigraph::impl::VertexId; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/v_overlaps.cpp:142:26: required from here 142 | helper.DeleteLink(vertex, out_edge); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/construction_helper.hpp:118:14: warning: unused variable 'res' [-Wunused-variable] 118 | bool res = graph_.vertex(v).RemoveOutgoingEdge(e); | ^~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/observable_graph.hpp:13, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/edge_index_refiller.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/edge_index.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/sequence_mapper.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/test_utils.cpp:10: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 508 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/test_utils.cpp:122:55: required from here 122 | for (auto it = g.SmartEdgeBegin(); !it.IsEnd(); ++it) { | ^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/observable_graph.hpp:13, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/graph_simplification.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/simplification_test.cpp:12: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 508 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/parallel_processing.hpp:378:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity; size_t = long unsigned int]' 378 | for (; !it_.IsEnd(); ++it_) { | ^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/simplification_test.cpp:276:16: required from here 276 | remover.Run(); | ~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa_reader.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/v_overlaps.cpp:10: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp: In member function 'size_t debruijn_graph::DeBruijnGraph::link_length(VertexId, EdgeId, EdgeId) const': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp:142:5: warning: control reaches end of non-void function [-Wreturn-type] 142 | } | ^ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap >]' 508 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/graph_processing_algorithm.hpp:60:87: required from 'bool omnigraph::EdgeProcessingAlgorithm::Run(const Priority&, ProceedConditionT) [with Priority = omnigraph::LengthComparator; Graph = debruijn_graph::DeBruijnGraph; ProceedConditionT = func::TypedPredicate]' 60 | for (auto it = g_.SmartEdgeBegin(priority, conjugate_symmetry_); !it.IsEnd(); ++it) { | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/single_cell_simplification.hpp:45:38: required from 'bool debruijn::simplification::RemoveErroneousEdgesInLengthOrder(Graph&, func::TypedPredicate, size_t, std::function) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId; size_t = long unsigned int; typename Graph::EdgeId = omnigraph::impl::EdgeId]' 45 | return erroneous_edge_remover.Run(omnigraph::LengthComparator(g), | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 46 | omnigraph::LengthUpperBound(g, max_length)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/single_cell_simplification.hpp:63:45: required from 'bool debruijn::simplification::TopologyRemoveErroneousEdges(Graph&, const debruijn_graph::config::debruijn_config::simplification::topology_based_ec_remover&, std::function) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId]' 63 | return RemoveErroneousEdgesInLengthOrder(g, condition, max_length, removal_handler); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/simplification_test.cpp:223:72: required from here 223 | while(debruijn::simplification::TopologyRemoveErroneousEdges(g, tec_config, 0)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/stats/picture_dump.hpp:18, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/path_visualizer.hpp:13, from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/path_extend_test.cpp:9: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:30:10: required from here 30 | bool Load(const std::string &basename, Graph &graph) override { | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:31:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 31 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:43:10: required from here 43 | bool BinRead(std::istream &is, Graph &graph) override { | ^~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:44:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 44 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:10: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:47:10: required from here 47 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:61:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 61 | auto new_id = graph.AddVertex(typename Graph::VertexData(graph.k()), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:83:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 83 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/chimera_stats.hpp:13, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/graph_simplification.hpp:12: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp: In instantiation of 'void omnigraph::simplification::relative_coverage::Component::RemoveFromBorder(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp:85:9: required from 'void omnigraph::simplification::relative_coverage::Component::MakeInner(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' 85 | RemoveFromBorder(v); | ^~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp:506:37: required from 'bool omnigraph::simplification::relative_coverage::component_remover::InnerComponentSearcher::FindComponent() [with Graph = debruijn_graph::DeBruijnGraph]' 506 | component_.MakeInner(v); | ~~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp:669:49: required from 'std::optional > omnigraph::simplification::relative_coverage::component_remover::RelativeCovComponentFinder::operator()(EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]' 669 | if (component_searcher.FindComponent()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp:722:61: required from 'omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover::RelativeCoverageComponentRemover(Graph&, size_t, const omnigraph::FlankingCoverage&, double, size_t, size_t, size_t, double, HandlerF, size_t, std::filesystem::__cxx11::path) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int; HandlerF = std::function, std::allocator >&)>]' 722 | [&](EdgeId e) { return static_cast(finder_(e)); }, chunk_cnt); | ~~~~~~~^~~ /usr/include/c++/14/bits/stl_construct.h:119:7: required from 'constexpr void std::_Construct(_Tp*, _Args&& ...) [with _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, function, allocator >&)>&, const long unsigned int&, filesystem::__cxx11::path&}]' 119 | ::new((void*)__p) _Tp(std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/alloc_traits.h:706:19: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /usr/include/c++/14/bits/shared_ptr_base.h:969:16: required from 'std::__shared_count<_Lp>::__shared_count(_Tp*&, std::_Sp_alloc_shared_tag<_Alloc>, _Args&& ...) [with _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; _Alloc = std::allocator; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::filesystem::__cxx11::path&}; __gnu_cxx::_Lock_policy _Lp = __gnu_cxx::_S_atomic]' 969 | auto __pi = ::new (__mem) | ^~~~~~~~~~~~~ 970 | _Sp_cp_type(__a._M_a, std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/shared_ptr_base.h:1713:14: required from 'std::__shared_ptr<_Tp, _Lp>::__shared_ptr(std::_Sp_alloc_shared_tag<_Tp>, _Args&& ...) [with _Alloc = std::allocator; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::filesystem::__cxx11::path&}; _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; __gnu_cxx::_Lock_policy _Lp = __gnu_cxx::_S_atomic]' 1713 | : _M_ptr(), _M_refcount(_M_ptr, __tag, std::forward<_Args>(__args)...) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/shared_ptr.h:463:59: required from 'std::shared_ptr<_Tp>::shared_ptr(std::_Sp_alloc_shared_tag<_Tp>, _Args&& ...) [with _Alloc = std::allocator; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::filesystem::__cxx11::path&}; _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover]' 463 | : __shared_ptr<_Tp>(__tag, std::forward<_Args>(__args)...) | ^ /usr/include/c++/14/bits/shared_ptr.h:1007:14: required from 'std::shared_ptr > std::make_shared(_Args&& ...) [with _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, function, allocator >&)>&, const long unsigned int&, filesystem::__cxx11::path&}; _NonArray<_Tp> = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover]' 1007 | return shared_ptr<_Tp>(_Sp_alloc_shared_tag<_Alloc>{__a}, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1008 | std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/graph_simplification.hpp:438:49: required from 'omnigraph::AlgoPtr debruijn::simplification::RelativeCoverageComponentRemoverInstance(Graph&, const omnigraph::FlankingCoverage&, const debruijn_graph::config::debruijn_config::simplification::relative_coverage_comp_remover&, const SimplifInfoContainer&, typename omnigraph::ComponentRemover::HandlerF) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::AlgoPtr = std::shared_ptr >; typename omnigraph::ComponentRemover::HandlerF = std::function, std::allocator >&)>]' 437 | return std::make_shared>(g, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 439 | info.chunk_cnt(), | ~~~~~~~~~~~~~~~~~ 440 | flanking_cov, | ~~~~~~~~~~~~~ 441 | rcc_config.coverage_gap, | ~~~~~~~~~~~~~~~~~~~~~~~~ 442 | size_t(double(info.read_length()) * rcc_config.length_coeff), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 443 | size_t(double(info.read_length()) * rcc_config.tip_allowing_length_coeff), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 444 | connecting_path_length_bound, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 445 | max_coverage, | ~~~~~~~~~~~~~ 446 | removal_handler, rcc_config.vertex_count_limit, pics_dir); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/simplification_test.cpp:313:83: required from here 313 | auto algo = debruijn::simplification::RelativeCoverageComponentRemoverInstance(graph, flanking_cov, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 314 | standard_rcc_config(), | ~~~~~~~~~~~~~~~~~~~~~~ 315 | standard_simplif_relevant_info()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp:55:16: warning: unused variable 'cnt' [-Wunused-variable] 55 | size_t cnt = border_.erase(v); | ^~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/graph_simplification.hpp:19: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/bulge_remover.hpp: In instantiation of 'omnigraph::ParallelBulgeRemover::SmartEdgeSet omnigraph::ParallelBulgeRemover::RetainIndependentBulges(std::vector&) const [with Graph = debruijn_graph::DeBruijnGraph; SmartEdgeSet = omnigraph::SmartSetIterator >]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/bulge_remover.hpp:721:42: required from 'size_t omnigraph::ParallelBulgeRemover::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 721 | auto interacting_edges = RetainIndependentBulges(bulges); | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/bulge_remover.hpp:678:12: required from here 678 | size_t Run(bool force_primary_launch, double /*iter_run_progress*/) override { | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/bulge_remover.hpp:582:16: warning: unused variable 'total_cnt' [-Wunused-variable] 582 | size_t total_cnt = bulges.size(); | ^~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap >]' 508 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/parallel_processing.hpp:378:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator; size_t = long unsigned int]' 378 | for (; !it_.IsEnd(); ++it_) { | ^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/parallel_processing.hpp:354:12: required from here 354 | size_t Run(bool force_primary_launch = false, | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_tip_clipper.hpp:14, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/graph_simplification.hpp:18: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/dominated_set_finder.hpp: In instantiation of 'Range omnigraph::DominatedSetFinder::NeighbourDistanceRange(VertexId, bool) const [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/dominated_set_finder.hpp:107:23: required from 'bool omnigraph::DominatedSetFinder::FillDominated() [with Graph = debruijn_graph::DeBruijnGraph]' 107 | Range r = NeighbourDistanceRange(v); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:989:43: required from 'omnigraph::complex_br::LocalizedComponentFinder::LocalizedComponentFinder(const Graph&, size_t, size_t, VertexId) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int; VertexId = omnigraph::impl::VertexId]' 989 | dominated_set_finder.FillDominated(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1058:41: required from 'bool omnigraph::complex_br::CandidateFinder::Check(VertexId) const [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' 1058 | LocalizedComponentFinder comp_finder(g, max_length_, | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1056:10: required from here 1056 | bool Check(VertexId v) const override { | ^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/dominated_set_finder.hpp:50:51: warning: unused parameter 'dominated_only' [-Wunused-parameter] 50 | Range NeighbourDistanceRange(VertexId v, bool dominated_only = true) const { | ~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/graph_simplification.hpp:20: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'bool omnigraph::complex_br::ComponentProjector::SplitComponent() [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:812:14: required from 'bool omnigraph::complex_br::ComponentProjector::ProjectComponent() [with Graph = debruijn_graph::DeBruijnGraph]' 812 | if (!SplitComponent()) { | ^~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1120:44: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::ProcessComponent(omnigraph::complex_br::LocalizedComponent&, size_t) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 1120 | if (!projector.ProjectComponent()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1147:17: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::InnerProcess(VertexId, std::vector&) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId; typename Graph::VertexId = omnigraph::impl::VertexId; typename Graph::VertexId = omnigraph::impl::VertexId]' 1147 | if (ProcessComponent(component, candidate_cnt)) { | ^~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1193:13: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::Process(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' 1193 | if (InnerProcess(v, vertices_to_post_process)) { | ^~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1187:10: required from here 1187 | bool Process(VertexId v) override { | ^~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:776:26: warning: variable 'inner_v' set but not used [-Wunused-but-set-variable] 776 | VertexId inner_v = g_.EdgeEnd(split_res.first); | ^~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'omnigraph::complex_br::ComponentProjector::EdgeId omnigraph::complex_br::ComponentProjector::CorrespondingTreeEdge(EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:823:29: required from 'bool omnigraph::complex_br::ComponentProjector::ProjectComponent() [with Graph = debruijn_graph::DeBruijnGraph]' 823 | EdgeId target = CorrespondingTreeEdge(*it); | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1120:44: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::ProcessComponent(omnigraph::complex_br::LocalizedComponent&, size_t) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 1120 | if (!projector.ProjectComponent()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1147:17: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::InnerProcess(VertexId, std::vector&) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId; typename Graph::VertexId = omnigraph::impl::VertexId; typename Graph::VertexId = omnigraph::impl::VertexId]' 1147 | if (ProcessComponent(component, candidate_cnt)) { | ^~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1193:13: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::Process(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' 1193 | if (InnerProcess(v, vertices_to_post_process)) { | ^~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1187:10: required from here 1187 | bool Process(VertexId v) override { | ^~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:792:16: warning: unused variable 'end_height' [-Wunused-variable] 792 | size_t end_height = component_.avg_distance(g_.EdgeEnd(e)); | ^~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 508 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:821:43: required from 'bool omnigraph::complex_br::ComponentProjector::ProjectComponent() [with Graph = debruijn_graph::DeBruijnGraph]' 821 | gc.e_end()); !it.IsEnd(); ++it) { | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1120:44: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::ProcessComponent(omnigraph::complex_br::LocalizedComponent&, size_t) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 1120 | if (!projector.ProjectComponent()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1147:17: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::InnerProcess(VertexId, std::vector&) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId; typename Graph::VertexId = omnigraph::impl::VertexId; typename Graph::VertexId = omnigraph::impl::VertexId]' 1147 | if (ProcessComponent(component, candidate_cnt)) { | ^~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1193:13: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::Process(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' 1193 | if (InnerProcess(v, vertices_to_post_process)) { | ^~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1187:10: required from here 1187 | bool Process(VertexId v) override { | ^~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'void omnigraph::complex_br::SkeletonTree::HandleDelete(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:310:10: required from here 310 | void HandleDelete(VertexId v) override { | ^~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:310:32: warning: unused parameter 'v' [-Wunused-parameter] 310 | void HandleDelete(VertexId v) override { | ~~~~~~~~~^ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'void omnigraph::complex_br::SkeletonTree::HandleMerge(const std::vector&, EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:321:10: required from here 321 | void HandleMerge(const std::vector &old_edges, EdgeId /*new_edge*/) override { | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:323:21: warning: variable 'e' set but not used [-Wunused-but-set-variable] 323 | for (EdgeId e : old_edges) { | ^ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'void omnigraph::complex_br::ComponentColoring::HandleGlue(EdgeId, EdgeId, EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:477:18: required from here 477 | virtual void HandleGlue(EdgeId /*new_edge*/, EdgeId edge1, EdgeId edge2) { | ^~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:477:71: warning: unused parameter 'edge2' [-Wunused-parameter] 477 | virtual void HandleGlue(EdgeId /*new_edge*/, EdgeId edge1, EdgeId edge2) { | ~~~~~~~^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'void omnigraph::complex_br::LocalizedComponent::HandleSplit(EdgeId, EdgeId, EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:242:18: required from here 242 | virtual void HandleSplit(EdgeId old_edge, EdgeId new_edge_1, EdgeId /*new_edge_2*/) { | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:245:18: warning: variable 'end' set but not used [-Wunused-but-set-variable] 245 | VertexId end = g_.EdgeEnd(old_edge); | ^~~ In file included from /usr/include/c++/14/string:51, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/perf/perfcounter.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/logger/logger.hpp:14, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/construction_helper.hpp:10: In static member function 'static void std::__copy_move::__assign_one(_Tp*, _Up*) [with _Tp = long unsigned int; _Up = const long unsigned int]', inlined from 'static constexpr _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const long unsigned int; _Up = long unsigned int; bool _IsMove = false]' at /usr/include/c++/14/bits/stl_algobase.h:455:20, inlined from 'constexpr _OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const long unsigned int*; _OI = long unsigned int*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30, inlined from 'constexpr _OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const long unsigned int*; _OI = long unsigned int*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42, inlined from 'constexpr _OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = const long unsigned int*; _OI = long unsigned int*]' at /usr/include/c++/14/bits/stl_algobase.h:555:31, inlined from 'constexpr _OI std::copy(_II, _II, _OI) [with _II = const long unsigned int*; _OI = long unsigned int*]' at /usr/include/c++/14/bits/stl_algobase.h:651:7, inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = const long unsigned int*; _ForwardIterator = long unsigned int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:147:27, inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = const long unsigned int*; _ForwardIterator = long unsigned int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, inlined from 'constexpr _ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = const long unsigned int*; _ForwardIterator = long unsigned int*; _Tp = long unsigned int]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, inlined from 'constexpr void std::vector<_Tp, _Alloc>::_M_range_initialize(_ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = const long unsigned int*; _Tp = long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:1697:33, inlined from 'constexpr std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:682:21, inlined from 'void PerformSplits(debruijn_graph::Graph&, std::ifstream&, const IdMapper&)' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/v_overlaps.cpp:133:51: /usr/include/c++/14/bits/stl_algobase.h:413:17: warning: 'split_link' may be used uninitialized [-Wmaybe-uninitialized] 413 | { *__to = *__from; } | ~~~~~~^~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/v_overlaps.cpp: In function 'void PerformSplits(debruijn_graph::Graph&, std::ifstream&, const IdMapper&)': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/v_overlaps.cpp:124:20: note: 'split_link' was declared here 124 | LinkId split_link; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/string:43, from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graphio.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/io_test.cpp:8: In member function 'void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = phmap::priv::Deallocate<8, std::allocator > > > > >(std::allocator > > > >*, void*, size_t)::M]', inlined from 'constexpr void std::allocator< >::deallocate(_Tp*, std::size_t) [with _Tp = phmap::priv::Deallocate<8, std::allocator > > > > >(std::allocator > > > >*, void*, size_t)::M]' at /usr/include/c++/14/bits/allocator.h:208:35, inlined from 'static void phmap::allocator_traits::deallocate(Alloc&, pointer, size_type) [with Alloc = std::allocator > > > > >(std::allocator > > > >*, void*, size_t)::M>]' at /usr/include/parallel_hashmap/phmap_base.h:1487:21, inlined from 'void phmap::priv::Deallocate(Alloc*, void*, size_t) [with long unsigned int Alignment = 8; Alloc = std::allocator > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:4210:17, inlined from 'void phmap::priv::btree::deallocate(size_type, node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2003:60, inlined from 'void phmap::priv::btree::delete_leaf_node(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2013:23, inlined from 'void phmap::priv::btree::internal_clear(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:3228:29, inlined from 'void phmap::priv::btree::clear() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2859:27, inlined from 'phmap::priv::btree::~btree() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:1704:18, inlined from 'phmap::priv::btree_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_container()' at /usr/include/parallel_hashmap/btree.h:3264:11, inlined from 'phmap::priv::btree_set_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_set_container()' at /usr/include/parallel_hashmap/btree.h:3429:11, inlined from 'phmap::priv::btree_map_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_map_container()' at /usr/include/parallel_hashmap/btree.h:3591:11, inlined from 'phmap::btree_map > >, phmap::Less, std::allocator > > > > >::~btree_map()' at /usr/include/parallel_hashmap/btree.h:3952:15, inlined from 'omnigraph::de::NoLockingAdapter > >, phmap::Less, std::allocator > > > > > >::~NoLockingAdapter()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info.hpp:536:7, inlined from 'std::pair > >, phmap::Less, std::allocator > > > > > > >::~pair()' at /usr/include/c++/14/bits/stl_pair.h:284:12, inlined from 'constexpr void std::destroy_at(_Tp*) [with _Tp = pair > >, phmap::Less, allocator > > > > > > >]' at /usr/include/c++/14/bits/stl_construct.h:88:18, inlined from 'static constexpr void std::allocator_traits >::destroy(allocator_type&, _Up*) [with _Up = std::pair > >, phmap::Less, std::allocator > > > > > > >; _Tp = std::pair > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/c++/14/bits/alloc_traits.h:599:19, inlined from 'static decltype (std::allocator_traits::destroy(a, p)) phmap::allocator_traits::destroy_impl(int, A&, T*) [with A = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; T = std::pair > >, phmap::Less, std::allocator > > > > > > >; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:1546:42, inlined from 'static void phmap::allocator_traits::destroy(Alloc&, T*) [with T = std::pair > >, phmap::Less, std::allocator > > > > > > >; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:1504:21, inlined from 'static void phmap::priv::map_slot_policy::swap(Allocator*, slot_type*, slot_type*) [with Allocator = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; K = omnigraph::impl::EdgeId; V = omnigraph::de::NoLockingAdapter > >, phmap::Less, std::allocator > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:4554:56, inlined from 'static void phmap::priv::common_params::swap(Alloc*, slot_type*, slot_type*) [with Key = omnigraph::impl::EdgeId; Compare = phmap::Less; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; int TargetNodeSize = 256; bool Multi = false; SlotPolicy = phmap::priv::map_slot_policy > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/parallel_hashmap/btree.h:888:30, inlined from 'void phmap::priv::btree_node::swap(phmap::priv::btree_node*, allocator_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > > > >, phmap::Less, std::allocator > >, phmap::Less, std::allocator > > > > > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2382:30: /usr/include/c++/14/bits/new_allocator.h:172:33: warning: 'void operator delete(void*, std::size_t)' called on unallocated object 'empty_node' [-Wfree-nonheap-object] 172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:15: /usr/include/parallel_hashmap/btree.h: In function 'void phmap::priv::btree_node::swap(phmap::priv::btree_node*, allocator_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > > > >, phmap::Less, std::allocator > >, phmap::Less, std::allocator > > > > > > > >, 256, false>]': /usr/include/parallel_hashmap/btree.h:1623:44: note: declared here 1623 | static constexpr EmptyNodeType empty_node( | ^~~~~~~~~~ [100%] Linking CXX executable ../../bin/debruijn_test cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/cmake -E cmake_link_script CMakeFiles/debruijn_test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/debruijn_test.dir/link.d CMakeFiles/debruijn_test.dir/graph_core_test.cpp.o CMakeFiles/debruijn_test.dir/histogram_test.cpp.o CMakeFiles/debruijn_test.dir/paired_info_test.cpp.o CMakeFiles/debruijn_test.dir/overlap_analysis_test.cpp.o CMakeFiles/debruijn_test.dir/simplification_test.cpp.o CMakeFiles/debruijn_test.dir/test_utils.cpp.o CMakeFiles/debruijn_test.dir/construction_test.cpp.o CMakeFiles/debruijn_test.dir/io_test.cpp.o CMakeFiles/debruijn_test.dir/path_extend_test.cpp.o CMakeFiles/debruijn_test.dir/graphio.cpp.o CMakeFiles/debruijn_test.dir/overlap_removal_test.cpp.o CMakeFiles/debruijn_test.dir/graph_alignment_test.cpp.o CMakeFiles/debruijn_test.dir/v_overlaps.cpp.o CMakeFiles/debruijn_test.dir/test.cpp.o "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/debruijn_test ../../common/libcommon_modules.a ../../common/io/libinput.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/io/graph/libgraphio.a ../../ext/teamcity_gtest/libteamcity_gtest.a -lgtest ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/kmer_index/libmph_index.a ../../common/modules/libmodules.a ../../common/configs/libconfigs.a ../../common/library/liblibrary.a ../../common/io/libinput.a ../../common/io/sam/libsamio.a ../../ext/samtools/libsamtools.a /usr/lib/x86_64-linux-gnu/libbamtools.so ../../common/io/binary/libbinary_io.a ../../common/alignment/libalignment.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/bwa/libbwa.a -lm ../../_deps/zlib_ng-build/libz.a ../../ext/lexy/src/liblexy_file.a make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [100%] Built target debruijn_test make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/Makefile2 include_test make[3]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/spades-4.0.0+dfsg1/src -B/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/CMakeFiles 42 make -f CMakeFiles/Makefile2 test/include_test/CMakeFiles/include_test.dir/all make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/coverage_model /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/coverage_model /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/coverage_model/CMakeFiles/coverage_model.dir/DependInfo.cmake "--color=" make -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/mimalloc /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/mimalloc/CMakeFiles/mimalloc-obj.dir/DependInfo.cmake "--color=" make -f _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/build.make _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/DependInfo.cmake "--color=" make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/depend make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/edlib /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/edlib /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/edlib/CMakeFiles/edlib.dir/DependInfo.cmake "--color=" make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/teamcity_gtest 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'/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/gqf/CMakeFiles/gqf.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/io/binary/CMakeFiles/binary_io.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/utils/CMakeFiles/version.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/kmer_index/CMakeFiles/mph_index.dir/build.make common/kmer_index/CMakeFiles/mph_index.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/kmer_index/CMakeFiles/mph_index.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 45%] Built target llvm-support [ 45%] Built target edlib [ 45%] Built target gqf [ 47%] Built target teamcity_gtest make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/depend [ 50%] Built target binary_io [ 52%] Built target version make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/DependInfo.cmake "--color=" make -f ext/bwa/CMakeFiles/bwa.dir/build.make ext/bwa/CMakeFiles/bwa.dir/depend [ 52%] Built target mph_index make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa/CMakeFiles/bwa.dir/DependInfo.cmake "--color=" make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/sequence /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/sequence/CMakeFiles/sequence.dir/DependInfo.cmake "--color=" make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/depend make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/samtools/CMakeFiles/samtools.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f ext/bwa/CMakeFiles/bwa.dir/build.make ext/bwa/CMakeFiles/bwa.dir/build make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/bwa/CMakeFiles/bwa.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/build [ 61%] Built target samtools make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/sequence/CMakeFiles/sequence.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/utils/CMakeFiles/utils.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 69%] Built target bwa make -f common/io/sam/CMakeFiles/samio.dir/build.make common/io/sam/CMakeFiles/samio.dir/depend [ 69%] Built target sequence make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/sam /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/sam /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/sam/CMakeFiles/samio.dir/DependInfo.cmake "--color=" [ 71%] Built target utils make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/io/sam/CMakeFiles/samio.dir/build.make common/io/sam/CMakeFiles/samio.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/io/sam/CMakeFiles/samio.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/build [ 71%] Built target samio make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/assembly_graph/CMakeFiles/assembly_graph.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/depend [ 73%] Built target assembly_graph make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/DependInfo.cmake "--color=" make -f common/alignment/CMakeFiles/alignment.dir/build.make common/alignment/CMakeFiles/alignment.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment/CMakeFiles/alignment.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/build make -f common/alignment/CMakeFiles/alignment.dir/build.make common/alignment/CMakeFiles/alignment.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/io/CMakeFiles/input.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/alignment/CMakeFiles/alignment.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 78%] Built target input [ 80%] Built target alignment make -f common/library/CMakeFiles/library.dir/build.make common/library/CMakeFiles/library.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/library /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/library /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/library/CMakeFiles/library.dir/DependInfo.cmake "--color=" make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/library/CMakeFiles/library.dir/build.make common/library/CMakeFiles/library.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/library/CMakeFiles/library.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/modules/CMakeFiles/modules.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 80%] Built target library make -f common/configs/CMakeFiles/configs.dir/build.make common/configs/CMakeFiles/configs.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/configs /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/configs /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/configs/CMakeFiles/configs.dir/DependInfo.cmake "--color=" [ 83%] Built target modules make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/configs/CMakeFiles/configs.dir/build.make common/configs/CMakeFiles/configs.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/configs/CMakeFiles/configs.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/paired_info/CMakeFiles/paired_info.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 85%] Built target paired_info [ 88%] Built target configs make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/modules/path_extend/CMakeFiles/path_extend.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 92%] Built target path_extend make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline/CMakeFiles/pipeline.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/pipeline/CMakeFiles/pipeline.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 92%] Built target pipeline make -f common/stages/CMakeFiles/stages.dir/build.make common/stages/CMakeFiles/stages.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/stages /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/stages/CMakeFiles/stages.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/stages/CMakeFiles/stages.dir/build.make common/stages/CMakeFiles/stages.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/stages/CMakeFiles/stages.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 95%] Built target stages make -f common/CMakeFiles/common_modules.dir/build.make common/CMakeFiles/common_modules.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/CMakeFiles/common_modules.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/CMakeFiles/common_modules.dir/build.make common/CMakeFiles/common_modules.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/CMakeFiles/common_modules.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 95%] Built target common_modules make -f test/include_test/CMakeFiles/include_test.dir/build.make test/include_test/CMakeFiles/include_test.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/include_test /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/include_test/CMakeFiles/include_test.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f test/include_test/CMakeFiles/include_test.dir/build.make test/include_test/CMakeFiles/include_test.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 95%] Building CXX object test/include_test/CMakeFiles/include_test.dir/seq_test.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools 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CMakeFiles/include_test.dir/seq_test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp [ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/sequence_test.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/include_test/CMakeFiles/include_test.dir/sequence_test.cpp.o -MF CMakeFiles/include_test.dir/sequence_test.cpp.o.d -o CMakeFiles/include_test.dir/sequence_test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/sequence_test.cpp [ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/rtseq_test.cpp.o [ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/quality_test.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include 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/build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/rtseq_test.cpp [ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/nucl_test.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/include_test/CMakeFiles/include_test.dir/quality_test.cpp.o -MF CMakeFiles/include_test.dir/quality_test.cpp.o.d -o CMakeFiles/include_test.dir/quality_test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/quality_test.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/include_test/CMakeFiles/include_test.dir/nucl_test.cpp.o -MF CMakeFiles/include_test.dir/nucl_test.cpp.o.d -o CMakeFiles/include_test.dir/nucl_test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/nucl_test.cpp [ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/cyclic_hash_test.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/include_test/CMakeFiles/include_test.dir/cyclic_hash_test.cpp.o -MF CMakeFiles/include_test.dir/cyclic_hash_test.cpp.o.d -o CMakeFiles/include_test.dir/cyclic_hash_test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/cyclic_hash_test.cpp [ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/binary_test.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/include_test/CMakeFiles/include_test.dir/binary_test.cpp.o -MF CMakeFiles/include_test.dir/binary_test.cpp.o.d -o CMakeFiles/include_test.dir/binary_test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/binary_test.cpp [100%] Building CXX object test/include_test/CMakeFiles/include_test.dir/test.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/include_test/CMakeFiles/include_test.dir/test.cpp.o -MF CMakeFiles/include_test.dir/test.cpp.o.d -o CMakeFiles/include_test.dir/test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/test.cpp In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:8: In member function 'char Seq::operator[](size_t) const [with long unsigned int size_ = 7; T = long unsigned int]', inlined from 'char Seq::first() const [with long unsigned int size_ = 7; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:462:26, inlined from 'virtual void Seq_TestFirstLast_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:157:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:228:68: warning: 's1$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 228 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_TestFirstLast_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:156:12: note: 's1$_M_elems$' was declared here 156 | Seq<7> s1("ACGTACT"); | ^~ In member function 'char Seq::operator[](size_t) const [with long unsigned int size_ = 7; T = long unsigned int]', inlined from 'char Seq::first() const [with long unsigned int size_ = 7; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:462:26, inlined from 'virtual void Seq_TestFirstLast_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:160:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:228:68: warning: 's2$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 228 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_TestFirstLast_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:159:12: note: 's2$_M_elems$' was declared here 159 | Seq<7> s2("TTTTTTT"); | ^~ In member function 'Seq Seq::operator<<(char) const [with long unsigned int size_ = 10; T = long unsigned int]', inlined from 'virtual void Seq_ShiftLeft_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:28:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:266:54: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 266 | data[DataSize - 1] = (data[DataSize - 1] >> 2) | ((T) c << lastnuclshift_); | ~~~~~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_ShiftLeft_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:27:13: note: 's$_M_elems$' was declared here 27 | Seq<10> s("ACGTACGTAC"); | ^ In member function 'Seq Seq::operator>>(char) const [with long unsigned int size_ = 10; T = long unsigned int]', inlined from 'virtual void Seq_ShiftRight_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:41:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:342:42: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 342 | res.data_[i] = (res.data_[i] << 2) | rm; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_ShiftRight_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:40:13: note: 's$_M_elems$' was declared here 40 | Seq<10> s("ACGTACGTAC"); | ^ In member function 'char Seq::operator[](size_t) const [with long unsigned int size_ = 10; T = long unsigned int]', inlined from 'std::string Seq::str() const [with long unsigned int size_ = 10; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:385:37, inlined from 'virtual void Seq_Str_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:55:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:228:39: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 228 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_Str_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:54:13: note: 's$_M_elems$' was declared here 54 | Seq<10> s("ACGTACGTAC"); | ^ In member function 'char Seq::operator[](size_t) const [with long unsigned int size_ = 10; T = long unsigned int]', inlined from 'Seq::Seq(const S&, size_t, size_t, bool) [with S = Seq<10>; long unsigned int size_ = 9; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:200:35, inlined from 'virtual void Seq_HeadAndTail_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:62:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:228:39: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 228 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_HeadAndTail_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:61:13: note: 's$_M_elems$' was declared here 61 | Seq<10> s("ACGTACGTAC"); | ^ In member function 'void Seq::set(size_t, char) [with long unsigned int size_ = 10; T = long unsigned int]', inlined from 'Seq Seq::operator!() const [with long unsigned int size_ = 10; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:241:20, inlined from 'virtual void Seq_ReverseComplement_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:138:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:358:40: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 358 | (data_[i >> TNuclBits] & ~((T) 3 << ((i & (TNucl - 1)) << 1))) | ((T) c << ((i & (TNucl - 1)) << 1)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_ReverseComplement_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:137:13: note: 's$_M_elems$' was declared here 137 | Seq<10> s("ACGTACGTAC"); | ^ In member function 'void Seq::set(size_t, char) [with long unsigned int size_ = 9; T = long unsigned int]', inlined from 'Seq Seq::operator!() const [with long unsigned int size_ = 9; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:241:20, inlined from 'virtual void Seq_ReverseComplement_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:142:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:358:40: warning: 's3$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 358 | (data_[i >> TNuclBits] & ~((T) 3 << ((i & (TNucl - 1)) << 1))) | ((T) c << ((i & (TNucl - 1)) << 1)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_ReverseComplement_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:141:12: note: 's3$_M_elems$' was declared here 141 | Seq<9> s3("ACGTACGTA"); | ^~ In member function 'char Seq::operator[](size_t) const [with long unsigned int size_ = 10; T = long unsigned int]', inlined from 'Seq::Seq(const S&, size_t, size_t, bool) [with S = Seq<10>; long unsigned int size_ = 5; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:200:35, inlined from 'virtual void Seq_FromBiggerSeq_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:68:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:228:39: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 228 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_FromBiggerSeq_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:67:13: note: 's$_M_elems$' was declared here 67 | Seq<10> s("ACGTACGTAC"); | ^ In member function 'char Seq::operator[](size_t) const [with long unsigned int size_ = 5; T = long unsigned int]', inlined from 'Seq::Seq(const S&, size_t, size_t, bool) [with S = Seq<5>; long unsigned int size_ = 4; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:200:35, inlined from 'Seq Seq::end() const [with long unsigned int size2_ = 4; T2 = long unsigned int; long unsigned int size_ = 5; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:445:16, inlined from 'virtual void Seq_End_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:116:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:228:39: warning: 's1$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 228 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_End_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:115:12: note: 's1$_M_elems$' was declared here 115 | Seq<5> s1("ACGTA"); | ^~ In member function 'char Seq::operator[](size_t) const [with long unsigned int size_ = 5; T = long unsigned int]', inlined from 'Seq::Seq(const S&, size_t, size_t, bool) [with S = Seq<5>; long unsigned int size_ = 4; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:200:35, inlined from 'Seq Seq::start() const [with long unsigned int size2_ = 4; T2 = long unsigned int; long unsigned int size_ = 5; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:439:16, inlined from 'virtual void Seq_Start_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:121:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:228:39: warning: 's1$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 228 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_Start_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:120:12: note: 's1$_M_elems$' was declared here 120 | Seq<5> s1("ACGTA"); | ^~ In member function 'Seq<(size_ + 1), T> Seq::pushBack(char) const [with long unsigned int size_ = 4; T = long unsigned int]', inlined from 'virtual void Seq_PushBack_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:80:9: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:288:59: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 288 | s.data_[s.DataSize - 1] = s.data_[s.DataSize - 1] | ((T) c << ((size_ & (TNucl - 1)) << 1)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_PushBack_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:79:16: note: 's$_M_elems$' was declared here 79 | Seq<4> s("ACGT"); | ^ In file included from /usr/include/gtest/gtest.h:71, from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:13: /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:84:38: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 84 | EXPECT_EQ("ACGTC", s.pushBack('C').str()); | ~~~~~~~~~~^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:83:31: note: 's$_M_elems$' was declared here 83 | Seq<4, unsigned char> s("ACGT"); | ^ In member function 'Seq<(size_ + 1), T> Seq::pushBack(char) const [with long unsigned int size_ = 3; T = long unsigned int]', inlined from 'virtual void Seq_PushBack_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:88:9: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:288:59: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 288 | s.data_[s.DataSize - 1] = s.data_[s.DataSize - 1] | ((T) c << ((size_ & (TNucl - 1)) << 1)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_PushBack_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:87:16: note: 's$_M_elems$' was declared here 87 | Seq<3> s("ACG"); | ^ In member function 'Seq Seq::operator<<(char) const [with long unsigned int size_ = 16; T = long unsigned int]', inlined from 'virtual void Seq_Test16_2_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:152:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:266:54: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 266 | data[DataSize - 1] = (data[DataSize - 1] >> 2) | ((T) c << lastnuclshift_); | ~~~~~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_Test16_2_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:151:13: note: 's$_M_elems$' was declared here 151 | Seq<16> s("TTTTTTTTTTTTTTTT"); | ^ In member function 'Seq Seq::operator<<(char) const [with long unsigned int size_ = 16; T = long unsigned int]', inlined from 'virtual void Seq_Test16_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:147:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:266:54: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 266 | data[DataSize - 1] = (data[DataSize - 1] >> 2) | ((T) c << lastnuclshift_); | ~~~~~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_Test16_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:146:13: note: 's$_M_elems$' was declared here 146 | Seq<16> s("AAAAAAAAAAAAAAAA"); | ^ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:20, from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/rtseq_test.cpp:8: In member function 'char Seq::operator[](size_t) const [with long unsigned int size_ = 5; T = long unsigned int]', inlined from 'std::string Seq::str() const [with long unsigned int size_ = 5; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:385:37, inlined from 'virtual void RtSeq_FromSeq_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/rtseq_test.cpp:337:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:228:39: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 228 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/rtseq_test.cpp: In member function 'virtual void RtSeq_FromSeq_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/rtseq_test.cpp:329:12: note: 's$_M_elems$' was declared here 329 | Seq<5> s("CGTAC"); | ^ In member function 'char Seq::operator[](size_t) const [with long unsigned int size_ = 10; T = long unsigned int]', inlined from 'std::string Seq::str() const [with long unsigned int size_ = 10; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:385:37, inlined from 'virtual void RtSeq_FromSeq_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/rtseq_test.cpp:338:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:228:39: warning: 's1$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 228 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/rtseq_test.cpp: In member function 'virtual void RtSeq_FromSeq_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/rtseq_test.cpp:330:13: note: 's1$_M_elems$' was declared here 330 | Seq<10> s1("ACGTACGTAC"); | ^~ In member function 'char Seq::operator[](size_t) const [with long unsigned int size_ = 16; T = long unsigned int]', inlined from 'std::string Seq::str() const [with long unsigned int size_ = 16; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:385:37, inlined from 'virtual void RtSeq_FromSeq_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/rtseq_test.cpp:339:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:228:39: warning: 's2$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 228 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/rtseq_test.cpp: In member function 'virtual void RtSeq_FromSeq_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/rtseq_test.cpp:331:13: note: 's2$_M_elems$' was declared here 331 | Seq<16> s2("CCCCGTACGTACGTAC"); | ^~ In member function 'char Seq::operator[](size_t) const [with long unsigned int size_ = 32; T = long unsigned int]', inlined from 'std::string Seq::str() const [with long unsigned int size_ = 32; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:385:37, inlined from 'virtual void RtSeq_FromSeq_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/rtseq_test.cpp:340:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:228:39: warning: 's3$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 228 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/rtseq_test.cpp: In member function 'virtual void RtSeq_FromSeq_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/rtseq_test.cpp:332:13: note: 's3$_M_elems$' was declared here 332 | Seq<32> s3("ACGTACGTACACGTACGTACACGTACGTACAC"); | ^~ [100%] Linking CXX executable ../../bin/include_test cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/include_test && /usr/bin/cmake -E cmake_link_script CMakeFiles/include_test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/include_test.dir/link.d CMakeFiles/include_test.dir/seq_test.cpp.o CMakeFiles/include_test.dir/sequence_test.cpp.o CMakeFiles/include_test.dir/rtseq_test.cpp.o CMakeFiles/include_test.dir/quality_test.cpp.o CMakeFiles/include_test.dir/nucl_test.cpp.o CMakeFiles/include_test.dir/cyclic_hash_test.cpp.o CMakeFiles/include_test.dir/binary_test.cpp.o CMakeFiles/include_test.dir/test.cpp.o "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/include_test ../../common/libcommon_modules.a ../../common/io/libinput.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/teamcity_gtest/libteamcity_gtest.a -lgtest ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/kmer_index/libmph_index.a ../../common/modules/libmodules.a ../../common/configs/libconfigs.a ../../common/library/liblibrary.a ../../common/io/libinput.a ../../common/io/sam/libsamio.a ../../ext/samtools/libsamtools.a /usr/lib/x86_64-linux-gnu/libbamtools.so ../../common/io/binary/libbinary_io.a ../../common/alignment/libalignment.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/bwa/libbwa.a ../../_deps/zlib_ng-build/libz.a -lm make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [100%] Built target include_test make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[2]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[1]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1' dh_auto_test -O--sourcedirectory=src -O--buildsystem=cmake cd obj-x86_64-linux-gnu && make -j12 test ARGS\+=--verbose ARGS\+=-j12 make[1]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' Running tests... /usr/bin/ctest --force-new-ctest-process --verbose -j12 UpdateCTestConfiguration from :/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/DartConfiguration.tcl Test project /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end Connected to MAKE jobserver test 1 Start 1: include_test 1: Test command: /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/bin/include_test 1: Working Directory: /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/include_test 1: Test timeout computed to be: 10000000 test 2 Start 2: debruijn_test 2: Test command: /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/bin/debruijn_test 2: Working Directory: /build/reproducible-path/spades-4.0.0+dfsg1/src/.. 2: Test timeout computed to be: 10000000 1: Running main() from gtest_main.cpp 1: [==========] Running 58 tests from 7 test suites. 1: [----------] Global test environment set-up. 1: [----------] 20 tests from Seq 1: [ RUN ] Seq.Selector 1: [ OK ] Seq.Selector (0 ms) 1: [ RUN ] Seq.ShiftLeft 1: [ OK ] Seq.ShiftLeft (0 ms) 1: [ RUN ] Seq.ShiftRight 1: [ OK ] Seq.ShiftRight (0 ms) 1: [ RUN ] Seq.Str 1: [ OK ] Seq.Str (0 ms) 1: [ RUN ] Seq.HeadAndTail 1: [ OK ] Seq.HeadAndTail (0 ms) 1: [ RUN ] Seq.FromBiggerSeq 1: [ OK ] Seq.FromBiggerSeq (0 ms) 1: [ RUN ] Seq.FromType 1: [ OK ] Seq.FromType (0 ms) 1: [ RUN ] Seq.PushBack 1: [ OK ] Seq.PushBack (0 ms) 1: [ RUN ] Seq.Null 1: [ OK ] Seq.Null (0 ms) 1: [ RUN ] Seq.EndNull 1: [ OK ] Seq.EndNull (0 ms) 1: [ RUN ] Seq.StartNull 1: [ OK ] Seq.StartNull (0 ms) 1: [ RUN ] Seq.AddSymbolForNullValue 1: [ OK ] Seq.AddSymbolForNullValue (0 ms) 1: [ RUN ] Seq.End 1: [ OK ] Seq.End (0 ms) 1: [ RUN ] Seq.Start 1: [ OK ] Seq.Start (0 ms) 1: [ RUN ] Seq.Complex 1: [ OK ] Seq.Complex (0 ms) 1: [ RUN ] Seq.FromCharArray 1: [ OK ] Seq.FromCharArray (0 ms) 1: [ RUN ] Seq.ReverseComplement 1: [ OK ] Seq.ReverseComplement (0 ms) 1: [ RUN ] Seq.Test16 1: [ OK ] Seq.Test16 (0 ms) 1: [ RUN ] Seq.Test16_2 1: [ OK ] Seq.Test16_2 (0 ms) 1: [ RUN ] Seq.TestFirstLast 1: [ OK ] Seq.TestFirstLast (0 ms) 1: [----------] 20 tests from Seq (0 ms total) 1: 1: [----------] 6 tests from Sequence 1: [ RUN ] Sequence.Selector 1: [ OK ] Sequence.Selector (0 ms) 1: [ RUN ] Sequence.ZeroLength 1: [ OK ] Sequence.ZeroLength (0 ms) 1: [ RUN ] Sequence.NullValue 1: [ OK ] Sequence.NullValue (0 ms) 1: [ RUN ] Sequence.Sum 1: [ OK ] Sequence.Sum (0 ms) 1: [ RUN ] Sequence.Str 1: [ OK ] Sequence.Str (0 ms) 1: [ RUN ] Sequence.ReverseComplement 1: [ OK ] Sequence.ReverseComplement (0 ms) 1: [----------] 6 tests from Sequence (0 ms total) 1: 1: [----------] 23 tests from RtSeq 1: [ RUN ] RtSeq.Selector 1: [ OK ] RtSeq.Selector (0 ms) 1: [ RUN ] RtSeq.ShiftLeft 1: [ OK ] RtSeq.ShiftLeft (0 ms) 1: [ RUN ] RtSeq.ShiftLeftThis 1: [ OK ] RtSeq.ShiftLeftThis (0 ms) 1: [ RUN ] RtSeq.ShiftRight 1: [ OK ] RtSeq.ShiftRight (0 ms) 1: [ RUN ] RtSeq.ShiftRightThis 1: [ OK ] RtSeq.ShiftRightThis (0 ms) 1: [ RUN ] RtSeq.Str 1: [ OK ] RtSeq.Str (0 ms) 1: [ RUN ] RtSeq.HeadAndTail 1: [ OK ] RtSeq.HeadAndTail (0 ms) 1: [ RUN ] RtSeq.FromBiggerRtSeq 1: [ OK ] RtSeq.FromBiggerRtSeq (0 ms) 1: [ RUN ] RtSeq.FromSeq 1: [ OK ] RtSeq.FromSeq (0 ms) 1: [ RUN ] RtSeq.ToSeq 1: [ OK ] RtSeq.ToSeq (0 ms) 1: [ RUN ] RtSeq.FromType 1: [ OK ] RtSeq.FromType (0 ms) 1: [ RUN ] RtSeq.PushBack 1: [ OK ] RtSeq.PushBack (0 ms) 1: [ RUN ] RtSeq.PushBackThis 1: [ OK ] RtSeq.PushBackThis (0 ms) 1: [ RUN ] RtSeq.PushFront 1: [ OK ] RtSeq.PushFront (0 ms) 1: [ RUN ] RtSeq.PushFrontThis 1: [ OK ] RtSeq.PushFrontThis (0 ms) 1: [ RUN ] RtSeq.Null 1: [ OK ] RtSeq.Null (0 ms) 1: [ RUN ] RtSeq.AddSymbolForNullValue 1: [ OK ] RtSeq.AddSymbolForNullValue (0 ms) 1: [ RUN ] RtSeq.Complex 1: [ OK ] RtSeq.Complex (0 ms) 1: [ RUN ] RtSeq.FromCharArray 1: [ OK ] RtSeq.FromCharArray (0 ms) 1: [ RUN ] RtSeq.ReverseComplement 1: [ OK ] RtSeq.ReverseComplement (0 ms) 1: [ RUN ] RtSeq.16 1: [ OK ] RtSeq.16 (0 ms) 1: [ RUN ] RtSeq.16_2 1: [ OK ] RtSeq.16_2 (0 ms) 1: [ RUN ] RtSeq.FirstLast 1: [ OK ] RtSeq.FirstLast (0 ms) 1: [----------] 23 tests from RtSeq (0 ms total) 1: 1: [----------] 1 test from Quality 1: [ RUN ] Quality.Test 1: [ OK ] Quality.Test (0 ms) 1: [----------] 1 test from Quality (0 ms total) 1: 1: [----------] 1 test from Nucl 1: [ RUN ] Nucl.Test 1: [ OK ] Nucl.Test (0 ms) 1: [----------] 1 test from Nucl (0 ms total) 1: 1: [----------] 4 tests from CyclicHash 1: [ RUN ] CyclicHash.TestBasic 1: [ OK ] CyclicHash.TestBasic (0 ms) 1: [ RUN ] CyclicHash.TestBasicRtSeq 1: [ OK ] CyclicHash.TestBasicRtSeq (0 ms) 1: [ RUN ] CyclicHash.TestRC 1: [ OK ] CyclicHash.TestRC (0 ms) 1: [ RUN ] CyclicHash.TestRoll 1: [ OK ] CyclicHash.TestRoll (0 ms) 1: [----------] 4 tests from CyclicHash (0 ms total) 1: 1: [----------] 3 tests from Binary 1: [ RUN ] Binary.Simple 1: [ OK ] Binary.Simple (0 ms) 1: [ RUN ] Binary.Containers 1: [ OK ] Binary.Containers (0 ms) 1: [ RUN ] Binary.Variadic 1: [ OK ] Binary.Variadic (0 ms) 1: [----------] 3 tests from Binary (0 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 58 tests from 7 test suites ran. (0 ms total) 1: [ PASSED ] 58 tests. 2: Running main() from gtest_main.cpp 2: [==========] Running 100 tests from 11 test suites. 2: [----------] Global test environment set-up. 2: [----------] 6 tests from GraphCore 2: [ RUN ] GraphCore.Empty 1/2 Test #1: include_test ..................... Passed 0.02 sec 2: 0:00:00.000 1M / 9M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.024 1M / 9M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.Empty (31 ms) 2: [ RUN ] GraphCore.OneVertex 2: 0:00:00.032 1M / 9M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.040 1M / 9M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.OneVertex (23 ms) 2: [ RUN ] GraphCore.OneEdge 2: 0:00:00.055 1M / 9M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.063 1M / 9M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.OneEdge (23 ms) 2: [ RUN ] GraphCore.VertexMethods 2: 0:00:00.079 1M / 9M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.091 1M / 9M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.VertexMethods (28 ms) 2: [ RUN ] GraphCore.SmartIterator 2: 0:00:00.108 1M / 9M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.123 1M / 9M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.SmartIterator (32 ms) 2: [ RUN ] GraphCore.SelfRCEdgeMerge 2: 0:00:00.140 1M / 9M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.156 1M / 9M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.SelfRCEdgeMerge (31 ms) 2: [----------] 6 tests from GraphCore (171 ms total) 2: 2: [----------] 1 test from Histogram 2: [ RUN ] Histogram.StrongWeakPtrBasic 2: [ OK ] Histogram.StrongWeakPtrBasic (0 ms) 2: [----------] 1 test from Histogram (0 ms total) 2: 2: [----------] 13 tests from PairedInfo 2: [ RUN ] PairedInfo.Construct 2: [ OK ] PairedInfo.Construct (0 ms) 2: [ RUN ] PairedInfo.Access 2: [ OK ] PairedInfo.Access (0 ms) 2: [ RUN ] PairedInfo.HalfAccess 2: [ OK ] PairedInfo.HalfAccess (0 ms) 2: [ RUN ] PairedInfo.Remove 2: [ OK ] PairedInfo.Remove (0 ms) 2: [ RUN ] PairedInfo.UnexistingEdges 2: [ OK ] PairedInfo.UnexistingEdges (0 ms) 2: [ RUN ] PairedInfo.Prune 2: [ OK ] PairedInfo.Prune (0 ms) 2: [ RUN ] PairedInfo.Neighbours 2: [ OK ] PairedInfo.Neighbours (0 ms) 2: [ RUN ] PairedInfo.DoubledInfo 2: [ OK ] PairedInfo.DoubledInfo (0 ms) 2: [ RUN ] PairedInfo.HalfNeighbours 2: [ OK ] PairedInfo.HalfNeighbours (0 ms) 2: [ RUN ] PairedInfo.MoreNeighbours 2: [ OK ] PairedInfo.MoreNeighbours (0 ms) 2: [ RUN ] PairedInfo.Merge 2: [ OK ] PairedInfo.Merge (0 ms) 2: [ RUN ] PairedInfo.PairTraverse 2: [ OK ] PairedInfo.PairTraverse (0 ms) 2: [ RUN ] PairedInfo.RandomSymmetry 2: 0:00:00.172 1M / 9M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.187 1M / 9M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: [ OK ] PairedInfo.RandomSymmetry (57 ms) 2: [----------] 13 tests from PairedInfo (57 ms total) 2: 2: [----------] 13 tests from OverlapAnalysis 2: [ RUN ] OverlapAnalysis.Trivial 2: When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. 2: [ OK ] OverlapAnalysis.Trivial (0 ms) 2: [ RUN ] OverlapAnalysis.Mismatch 2: When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. 2: [ OK ] OverlapAnalysis.Mismatch (0 ms) 2: [ RUN ] OverlapAnalysis.Mismatch2 2: When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. 2: [ OK ] OverlapAnalysis.Mismatch2 (0 ms) 2: [ RUN ] OverlapAnalysis.Deletion 2: When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. 2: [ OK ] OverlapAnalysis.Deletion (0 ms) 2: [ RUN ] OverlapAnalysis.Insertion 2: When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. 2: [ OK ] OverlapAnalysis.Insertion (0 ms) 2: [ RUN ] OverlapAnalysis.QueryLonger 2: When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. 2: [ OK ] OverlapAnalysis.QueryLonger (0 ms) 2: [ RUN ] OverlapAnalysis.RefLonger 2: When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. 2: [ OK ] OverlapAnalysis.RefLonger (0 ms) 2: [ RUN ] OverlapAnalysis.TrivialBoundedFlank 2: When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. 2: [ OK ] OverlapAnalysis.TrivialBoundedFlank (0 ms) 2: [ RUN ] OverlapAnalysis.PartialPerfectAlignment 2: When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. 2: [ OK ] OverlapAnalysis.PartialPerfectAlignment (0 ms) 2: [ RUN ] OverlapAnalysis.Unalignable 2: When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. 2: [ OK ] OverlapAnalysis.Unalignable (0 ms) 2: [ RUN ] OverlapAnalysis.Large 2: [ OK ] OverlapAnalysis.Large (0 ms) 2: [ RUN ] OverlapAnalysis.SimpleGap 2: [ OK ] OverlapAnalysis.SimpleGap (0 ms) 2: [ RUN ] OverlapAnalysis.UndefinedBehavior 2: [ OK ] OverlapAnalysis.UndefinedBehavior (0 ms) 2: [----------] 13 tests from OverlapAnalysis (0 ms total) 2: 2: [----------] 17 tests from Simplification 2: [ RUN ] Simplification.SimpleTipClipperTest 2: 0:00:00.229 1M / 11M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.236 1M / 11M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.248 1M / 12M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip.grp 2: 0:00:00.264 1M / 12M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip started 2: 0:00:00.280 1M / 12M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip 2: [ OK ] Simplification.SimpleTipClipperTest (82 ms) 2: [ RUN ] Simplification.SimpleBulgeRemovalTest 2: 0:00:00.312 1M / 12M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.328 1M / 12M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.344 1M / 12M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge.grp 2: 0:00:00.360 1M / 12M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge started 2: 0:00:00.376 1M / 12M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge 2: 0:00:00.392 1M / 12M INFO General (graph_simplification.hpp : 657) Creating br instance 2: [ OK ] Simplification.SimpleBulgeRemovalTest (112 ms) 2: [ RUN ] Simplification.TipobulgeTest 2: 0:00:00.424 1M / 12M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.440 1M / 12M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.448 1M / 12M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge.grp 2: 0:00:00.448 1M / 12M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge started 2: 0:00:00.448 1M / 12M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge 2: 0:00:00.448 1M / 12M INFO General (graph_simplification.hpp : 657) Creating br instance 2: [ OK ] Simplification.TipobulgeTest (24 ms) 2: [ RUN ] Simplification.SimpleECTest 2: 0:00:00.448 1M / 12M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.448 1M / 12M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.448 1M / 12M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp 2: 0:00:00.448 1M / 12M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started 2: 0:00:00.457 623M / 623M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path 2: [ OK ] Simplification.SimpleECTest (50 ms) 2: [ RUN ] Simplification.SimpleIterECTest 2: 0:00:00.499 1M / 50M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.500 1M / 50M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.500 1M / 50M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp 2: 0:00:00.500 1M / 50M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started 2: 0:00:00.508 623M / 623M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path 2: [ OK ] Simplification.SimpleIterECTest (45 ms) 2: [ RUN ] Simplification.IterECTest 2: 0:00:00.544 1M / 51M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.548 1M / 51M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.548 1M / 51M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp 2: 0:00:00.548 1M / 51M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started 2: 0:00:00.556 623M / 623M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path 2: [ OK ] Simplification.IterECTest (54 ms) 2: [ RUN ] Simplification.IterUniquePath 2: 0:00:00.599 1M / 51M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.600 1M / 51M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.600 1M / 51M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp 2: 0:00:00.600 1M / 51M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started 2: 0:00:00.608 623M / 623M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path 2: 0:00:00.608 623M / 623M INFO General (single_cell_simplification: 56) Removing connections based on topology 2: 0:00:00.614 623M / 623M INFO General (single_cell_simplification: 56) Removing connections based on topology 2: [ OK ] Simplification.IterUniquePath (51 ms) 2: [ RUN ] Simplification.MFUniquePath 2: 0:00:00.650 1M / 51M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.652 1M / 51M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.652 1M / 51M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/unique_path.grp 2: 0:00:00.652 1M / 51M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/unique_path started 2: 0:00:00.658 606M / 606M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/unique_path 2: 0:00:00.660 606M / 606M INFO General (single_cell_simplification: 133) Removing connections based on max flow strategy 2: [ OK ] Simplification.MFUniquePath (54 ms) 2: [ RUN ] Simplification.ComplexBulgeRemoverOnSimpleBulge 2: 0:00:00.705 1M / 51M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.708 1M / 51M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.708 1M / 51M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge.grp 2: 0:00:00.708 1M / 51M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge started 2: 0:00:00.708 1M / 51M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge 2: 0:00:00.708 1M / 51M INFO General (simplification_test.cpp : 277) Done 2: [ OK ] Simplification.ComplexBulgeRemoverOnSimpleBulge (3 ms) 2: [ RUN ] Simplification.ComplexBulge 2: 0:00:00.709 1M / 51M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.709 1M / 51M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.709 1M / 51M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 2: 0:00:00.709 1M / 51M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge.grp 2: 0:00:00.709 1M / 51M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started 2: 0:00:00.723 1172M / 1172M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge 2: 0:00:00.724 1172M / 1172M INFO General (edge_index.hpp : 175) Using small index (max_id = 21626308) 2: 0:00:00.745 1172M / 1172M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:00.799 1172M / 1172M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 16969 kmers, 13008 bytes occupied (6.13259 bits per kmer). 2: 0:00:00.800 1172M / 1172M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. 2: 0:00:00.832 1172M / 1172M INFO General (graphio.cpp : 189) Reading edges positions, ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started 2: 0:00:00.848 1172M / 1172M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge 2: [ OK ] Simplification.ComplexBulge (233 ms) 2: [ RUN ] Simplification.BigComplexBulge 2: 0:00:00.942 1M / 55M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.948 1M / 55M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.964 1M / 55M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 2: 0:00:00.980 1M / 55M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge.grp 2: 0:00:00.996 1M / 55M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge started 2: 0:00:01.065 1160M / 1160M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge 2: 0:00:01.076 1160M / 1160M INFO General (edge_index.hpp : 175) Using small index (max_id = 21667994) 2: 0:00:01.131 1160M / 1160M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:01.516 1160M / 1160M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 65575 kmers, 48120 bytes occupied (5.87053 bits per kmer). 2: 0:00:01.532 1161M / 1161M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. 2: 0:00:01.580 1161M / 1161M INFO General (graphio.cpp : 189) Reading edges positions, ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge started 2: 0:00:01.596 1161M / 1161M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge 2: [ OK ] Simplification.BigComplexBulge (750 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover 2: 0:00:01.693 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.704 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.720 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 2: 0:00:01.732 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph.grp 2: 0:00:01.748 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph started 2: 0:00:01.764 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph 2: 0:00:01.780 1M / 159M INFO General (edge_index.hpp : 175) Using small index (max_id = 3036) 2: 0:00:01.811 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:01.854 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 100126 kmers, 73064 bytes occupied (5.83776 bits per kmer). 2: 0:00:01.864 2M / 159M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. 2: 0:00:01.896 2M / 159M INFO General (graphio.cpp : 189) Reading edges positions, ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph started 2: 0:00:01.912 2M / 159M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph 2: 0:00:01.928 2M / 159M INFO General (simplification_test.cpp : 309) Relative coverage component removal: 2: [ OK ] Simplification.RelativeCoverageRemover (295 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover1 2: 0:00:01.988 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.000 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:02.008 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 2: 0:00:02.013 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge.grp 2: 0:00:02.013 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started 2: 0:00:02.021 1172M / 1172M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge 2: 0:00:02.024 1172M / 1172M INFO General (edge_index.hpp : 175) Using small index (max_id = 21626308) 2: 0:00:02.050 1172M / 1172M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:02.127 1172M / 1172M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 16969 kmers, 13008 bytes occupied (6.13259 bits per kmer). 2: 0:00:02.132 1172M / 1172M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. 2: 0:00:02.161 1172M / 1172M INFO General (graphio.cpp : 189) Reading edges positions, ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started 2: 0:00:02.168 1172M / 1172M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge 2: 0:00:02.176 1172M / 1172M INFO General (simplification_test.cpp : 309) Relative coverage component removal: 2: [ OK ] Simplification.RelativeCoverageRemover1 (269 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover2 2: 0:00:02.258 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.260 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:02.260 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 2: 0:00:02.260 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph.grp 2: 0:00:02.260 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph started 2: 0:00:02.260 3M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph 2: 0:00:02.260 3M / 159M INFO General (edge_index.hpp : 175) Using small index (max_id = 35260) 2: 0:00:02.260 3M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:02.261 3M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 5034 kmers, 4400 bytes occupied (6.99245 bits per kmer). 2: 0:00:02.261 3M / 159M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. 2: 0:00:02.262 3M / 159M INFO General (graphio.cpp : 184) No positions were saved 2: 0:00:02.262 3M / 159M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph 2: 0:00:02.262 3M / 159M INFO General (simplification_test.cpp : 309) Relative coverage component removal: 2: [ OK ] Simplification.RelativeCoverageRemover2 (9 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover3 2: 0:00:02.268 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.276 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:02.276 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 2: 0:00:02.276 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge.grp 2: 0:00:02.276 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge started 2: 0:00:02.276 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge 2: 0:00:02.276 1M / 159M INFO General (edge_index.hpp : 175) Using small index (max_id = 12354) 2: 0:00:02.276 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:02.276 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 1318 kmers, 1728 bytes occupied (10.4886 bits per kmer). 2: 0:00:02.276 1M / 159M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. 2: 0:00:02.276 1M / 159M INFO General (graphio.cpp : 184) No positions were saved 2: 0:00:02.276 1M / 159M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge 2: 0:00:02.276 1M / 159M INFO General (simplification_test.cpp : 309) Relative coverage component removal: 2: [ OK ] Simplification.RelativeCoverageRemover3 (9 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover4 2: 0:00:02.277 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.277 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:02.277 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 2: 0:00:02.277 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge_2/graph.grp 2: 0:00:02.277 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge_2/graph started 2: 0:00:02.277 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge_2/graph 2: 0:00:02.277 4M / 159M INFO General (edge_index.hpp : 175) Using small index (max_id = 36400) 2: 0:00:02.278 4M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:02.281 4M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 14278 kmers, 11072 bytes occupied (6.20367 bits per kmer). 2: 0:00:02.292 4M / 159M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. 2: 0:00:02.297 4M / 159M INFO General (graphio.cpp : 184) No positions were saved 2: 0:00:02.297 4M / 159M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/tipobulge_2/graph 2: 0:00:02.297 4M / 159M INFO General (simplification_test.cpp : 309) Relative coverage component removal: 2: [ OK ] Simplification.RelativeCoverageRemover4 (29 ms) 2: [ RUN ] Simplification.CompressorTest 2: 0:00:02.306 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.308 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:02.312 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 2: 0:00:02.312 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/compression/graph.grp 2: 0:00:02.312 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/compression/graph started 2: 0:00:02.312 2M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/compression/graph 2: 0:00:02.312 2M / 159M INFO General (edge_index.hpp : 175) Using small index (max_id = 5512) 2: 0:00:02.312 2M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:02.312 2M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 295 kmers, 992 bytes occupied (26.9017 bits per kmer). 2: 0:00:02.312 2M / 159M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. 2: 0:00:02.312 2M / 159M INFO General (graphio.cpp : 184) No positions were saved 2: 0:00:02.312 2M / 159M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/compression/graph 2: [ OK ] Simplification.CompressorTest (6 ms) 2: [----------] 17 tests from Simplification (2083 ms total) 2: 2: [----------] 9 tests from GraphConstruction 2: [ RUN ] GraphConstruction.SimpleThread 2: 0:00:02.312 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.312 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:02.313 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 2: 0:00:02.313 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:02.313 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:02.313 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:02.313 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:02.328 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 2 reads 2: 0:00:02.335 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:02.344 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 6 kmers in total. 2: 0:00:02.360 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index 2: 0:00:02.367 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:02.376 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:02.392 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:02.392 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:02.411 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 6 kmers. 2: 0:00:02.412 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:02.412 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 7 kmers in total. 2: 0:00:02.412 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:02.413 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 7 kmers, 4800 bytes occupied (5485.71 bits per kmer). 2: 0:00:02.413 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. 2: 0:00:02.413 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers 2: 0:00:02.413 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. 2: 0:00:02.413 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph 2: 0:00:02.413 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths 2: 0:00:02.413 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 1 sequences extracted 2: 0:00:02.413 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops 2: 0:00:02.413 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected 2: 0:00:02.413 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... 2: 0:00:02.413 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted 2: 0:00:02.413 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 2 edges to create 2: 0:00:02.413 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records 2: 0:00:02.413 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records 2: 0:00:02.413 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done 2: 0:00:02.413 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... 2: 0:00:02.413 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted 2: 0:00:02.413 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 2 vertices to create 2: 0:00:02.413 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph 2: [ OK ] GraphConstruction.SimpleThread (102 ms) 2: [ RUN ] GraphConstruction.SimpleThread2 2: 0:00:02.415 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.415 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:02.415 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 2: 0:00:02.415 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:02.415 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:02.415 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:02.415 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:02.428 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 4 reads 2: 0:00:02.444 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:02.452 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 8 kmers in total. 2: 0:00:02.460 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index 2: 0:00:02.472 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:02.484 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:02.504 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:02.513 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:02.536 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 8 kmers. 2: 0:00:02.544 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:02.556 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 9 kmers in total. 2: 0:00:02.568 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:02.569 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 9 kmers, 6400 bytes occupied (5688.89 bits per kmer). 2: 0:00:02.569 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. 2: 0:00:02.672 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers 2: 0:00:02.688 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. 2: 0:00:02.696 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph 2: 0:00:02.708 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths 2: 0:00:02.743 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 1 sequences extracted 2: 0:00:02.775 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops 2: 0:00:02.799 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected 2: 0:00:02.816 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... 2: 0:00:02.831 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted 2: 0:00:02.848 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 2 edges to create 2: 0:00:02.863 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records 2: 0:00:02.895 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records 2: 0:00:02.912 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done 2: 0:00:02.928 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... 2: 0:00:02.943 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted 2: 0:00:02.959 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 2 vertices to create 2: 0:00:02.976 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph 2: [ OK ] GraphConstruction.SimpleThread2 (597 ms) 2: [ RUN ] GraphConstruction.SplitThread 2: 0:00:03.012 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:03.023 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:03.040 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 2: 0:00:03.056 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:03.072 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:03.104 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:03.120 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:03.160 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 4 reads 2: 0:00:03.168 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:03.184 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 11 kmers in total. 2: 0:00:03.200 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index 2: 0:00:03.216 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:03.232 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:03.264 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:03.280 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:03.312 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 11 kmers. 2: 0:00:03.328 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:03.336 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 12 kmers in total. 2: 0:00:03.344 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:03.352 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 12 kmers, 5600 bytes occupied (3733.33 bits per kmer). 2: 0:00:03.359 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. 2: 0:00:03.376 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers 2: 0:00:03.392 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. 2: 0:00:03.408 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph 2: 0:00:03.424 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths 2: 0:00:03.455 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 3 sequences extracted 2: 0:00:03.487 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops 2: 0:00:03.519 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected 2: 0:00:03.536 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... 2: 0:00:03.551 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted 2: 0:00:03.568 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 6 edges to create 2: 0:00:03.584 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records 2: 0:00:03.615 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records 2: 0:00:03.632 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done 2: 0:00:03.648 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... 2: 0:00:03.664 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted 2: 0:00:03.680 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 4 vertices to create 2: 0:00:03.695 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph 2: [ OK ] GraphConstruction.SplitThread (716 ms) 2: [ RUN ] GraphConstruction.SplitThread2 2: 0:00:03.728 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:03.744 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:03.760 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 2: 0:00:03.776 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:03.792 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:03.832 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:03.848 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:03.868 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 4 reads 2: 0:00:03.884 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:03.896 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 11 kmers in total. 2: 0:00:03.908 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index 2: 0:00:03.915 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:03.932 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:03.959 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:03.960 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:03.979 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 11 kmers. 2: 0:00:03.996 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:04.004 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 11 kmers in total. 2: 0:00:04.020 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:04.036 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 11 kmers, 5600 bytes occupied (4072.73 bits per kmer). 2: 0:00:04.051 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. 2: 0:00:04.068 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers 2: 0:00:04.084 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. 2: 0:00:04.100 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph 2: 0:00:04.116 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths 2: 0:00:04.147 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 4 sequences extracted 2: 0:00:04.163 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops 2: 0:00:04.163 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected 2: 0:00:04.163 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... 2: 0:00:04.163 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted 2: 0:00:04.163 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 8 edges to create 2: 0:00:04.171 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records 2: 0:00:04.172 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records 2: 0:00:04.172 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done 2: 0:00:04.172 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... 2: 0:00:04.172 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted 2: 0:00:04.172 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 4 vertices to create 2: 0:00:04.172 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph 2: [ OK ] GraphConstruction.SplitThread2 (443 ms) 2: [ RUN ] GraphConstruction.Buldge 2: 0:00:04.172 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:04.172 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:04.172 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 2: 0:00:04.172 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:04.172 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:04.172 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:04.172 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:04.188 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 4 reads 2: 0:00:04.204 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:04.220 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 12 kmers in total. 2: 0:00:04.236 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index 2: 0:00:04.251 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:04.268 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:04.300 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:04.304 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:04.331 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 12 kmers. 2: 0:00:04.336 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:04.348 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 12 kmers in total. 2: 0:00:04.364 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:04.368 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 12 kmers, 5600 bytes occupied (3733.33 bits per kmer). 2: 0:00:04.376 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. 2: 0:00:04.376 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers 2: 0:00:04.376 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. 2: 0:00:04.376 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph 2: 0:00:04.376 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths 2: 0:00:04.376 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 2 sequences extracted 2: 0:00:04.376 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops 2: 0:00:04.376 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected 2: 0:00:04.376 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... 2: 0:00:04.376 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted 2: 0:00:04.376 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 4 edges to create 2: 0:00:04.376 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records 2: 0:00:04.376 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records 2: 0:00:04.376 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done 2: 0:00:04.376 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... 2: 0:00:04.376 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted 2: 0:00:04.376 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 2 vertices to create 2: 0:00:04.376 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph 2: [ OK ] GraphConstruction.Buldge (227 ms) 2: [ RUN ] GraphConstruction.CondenseSimple 2: 0:00:04.400 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:04.404 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:04.404 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 2: 0:00:04.404 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:04.404 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:04.404 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:04.404 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:04.420 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 8 reads 2: 0:00:04.420 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:04.421 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 13 kmers in total. 2: 0:00:04.421 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index 2: 0:00:04.421 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:04.421 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:04.421 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:04.421 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:04.436 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 13 kmers. 2: 0:00:04.448 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:04.456 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 13 kmers in total. 2: 0:00:04.463 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:04.464 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). 2: 0:00:04.464 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. 2: 0:00:04.464 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers 2: 0:00:04.464 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. 2: 0:00:04.464 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph 2: 0:00:04.464 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths 2: 0:00:04.464 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 3 sequences extracted 2: 0:00:04.465 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops 2: 0:00:04.465 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected 2: 0:00:04.465 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... 2: 0:00:04.465 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted 2: 0:00:04.465 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 6 edges to create 2: 0:00:04.465 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records 2: 0:00:04.465 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records 2: 0:00:04.465 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done 2: 0:00:04.465 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... 2: 0:00:04.465 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted 2: 0:00:04.465 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 3 vertices to create 2: 0:00:04.465 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph 2: [ OK ] GraphConstruction.CondenseSimple (71 ms) 2: [ RUN ] GraphConstruction.TestKmerStoringIndex 2: 0:00:04.472 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:04.488 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:04.504 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 2: 0:00:04.520 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 2: 0:00:04.536 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:04.556 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:04.560 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:04.560 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:04.576 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 8 reads 2: 0:00:04.576 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:04.577 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 13 kmers in total. 2: 0:00:04.577 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index 2: 0:00:04.577 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:04.577 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:04.577 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:04.577 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:04.579 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 13 kmers. 2: 0:00:04.579 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:04.588 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 13 kmers in total. 2: 0:00:04.591 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:04.592 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). 2: 0:00:04.592 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. 2: 0:00:04.592 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers 2: 0:00:04.592 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. 2: 0:00:04.592 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph 2: 0:00:04.592 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths 2: 0:00:04.592 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 3 sequences extracted 2: 0:00:04.593 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops 2: 0:00:04.593 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected 2: 0:00:04.593 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... 2: 0:00:04.593 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted 2: 0:00:04.593 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 6 edges to create 2: 0:00:04.593 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records 2: 0:00:04.593 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records 2: 0:00:04.593 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done 2: 0:00:04.593 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... 2: 0:00:04.593 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted 2: 0:00:04.593 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 3 vertices to create 2: 0:00:04.593 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph 2: 0:00:04.600 1M / 159M INFO General (graph_construction.hpp : 80) Building index with from graph 2: 0:00:04.612 1M / 159M INFO General (edge_index.hpp : 175) Using small index (max_id = 9) 2: 0:00:04.627 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:04.651 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 13 kmers, 800 bytes occupied (492.308 bits per kmer). 2: 0:00:04.660 1M / 159M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. 2: [ OK ] GraphConstruction.TestKmerStoringIndex (212 ms) 2: [ RUN ] GraphConstruction.TestKmerFreeIndex 2: 0:00:04.684 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:04.692 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:04.708 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 2: 0:00:04.716 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 2: 0:00:04.716 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:04.716 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:04.716 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:04.716 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:04.727 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 8 reads 2: 0:00:04.740 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:04.744 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 13 kmers in total. 2: 0:00:04.744 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index 2: 0:00:04.744 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:04.744 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:04.744 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:04.744 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:04.767 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 13 kmers. 2: 0:00:04.772 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:04.784 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 13 kmers in total. 2: 0:00:04.797 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:04.812 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). 2: 0:00:04.820 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. 2: 0:00:04.828 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers 2: 0:00:04.844 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. 2: 0:00:04.852 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph 2: 0:00:04.860 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths 2: 0:00:04.882 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 3 sequences extracted 2: 0:00:04.882 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops 2: 0:00:04.883 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected 2: 0:00:04.883 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... 2: 0:00:04.883 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted 2: 0:00:04.883 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 6 edges to create 2: 0:00:04.883 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records 2: 0:00:04.883 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records 2: 0:00:04.883 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done 2: 0:00:04.883 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... 2: 0:00:04.883 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted 2: 0:00:04.883 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 3 vertices to create 2: 0:00:04.883 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph 2: 0:00:04.883 1M / 159M INFO General (graph_construction.hpp : 80) Building index with from graph 2: 0:00:04.883 1M / 159M INFO General (edge_index.hpp : 175) Using small index (max_id = 9) 2: 0:00:04.883 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:04.883 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 13 kmers, 800 bytes occupied (492.308 bits per kmer). 2: 0:00:04.883 1M / 159M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. 2: [ OK ] GraphConstruction.TestKmerFreeIndex (199 ms) 2: [ RUN ] GraphConstruction.SimpleTestEarlyPairedInfo 2: 0:00:04.883 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:04.883 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:04.883 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 2: 0:00:04.883 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=3 2: 0:00:04.883 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:04.883 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:04.883 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:04.883 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:04.900 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 4 reads 2: 0:00:04.900 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:04.901 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 5 kmers in total. 2: 0:00:04.901 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index 2: 0:00:04.901 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:04.901 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:04.901 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:04.901 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:04.916 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 5 kmers. 2: 0:00:04.928 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:04.941 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 6 kmers in total. 2: 0:00:04.947 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:04.952 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 6 kmers, 4000 bytes occupied (5333.33 bits per kmer). 2: 0:00:04.952 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. 2: 0:00:04.952 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers 2: 0:00:04.952 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. 2: 0:00:04.952 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph 2: 0:00:04.952 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths 2: 0:00:04.952 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 5 sequences extracted 2: 0:00:04.952 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops 2: 0:00:04.952 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected 2: 0:00:04.952 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... 2: 0:00:04.952 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted 2: 0:00:04.952 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 10 edges to create 2: 0:00:04.952 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records 2: 0:00:04.952 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records 2: 0:00:04.952 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done 2: 0:00:04.952 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... 2: 0:00:04.952 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted 2: 0:00:04.952 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 6 vertices to create 2: 0:00:04.952 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph 2: 0:00:04.954 1M / 159M INFO General (graph_construction.hpp : 80) Building index with from graph 2: 0:00:04.954 1M / 159M INFO General (edge_index.hpp : 175) Using small index (max_id = 13) 2: 0:00:04.954 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:04.954 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 5 kmers, 800 bytes occupied (1280 bits per kmer). 2: 0:00:04.954 1M / 159M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. 2: 0:00:04.954 1M / 159M INFO General (graph_construction.hpp : 94) Filling coverage index 2: 0:00:04.954 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:04.954 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 5 kmers, 3200 bytes occupied (5120 bits per kmer). 2: 0:00:04.954 1M / 159M INFO General (coverage_hash_map_builder.: 49) Collecting k-mer coverage information from reads, this takes a while. 2: 0:00:04.954 1M / 159M INFO General (graph_construction.hpp : 100) Filling coverage and flanking coverage from PHM 2: 0:00:04.954 1M / 159M INFO General (graph_pack_helpers.cpp : 54) Normalizing k-mer map. Total 0 kmers to process 2: 0:00:04.954 1M / 159M INFO General (graph_pack_helpers.cpp : 56) Normalizing done 2: 0:00:04.956 14M / 159M INFO General (sequence_mapper_notifier.h: 64) Starting sequence mapping 2: 0:00:04.965 14M / 159M INFO General (sequence_mapper_notifier.h: 103) Total 2 reads processed 2: [ OK ] GraphConstruction.SimpleTestEarlyPairedInfo (86 ms) 2: [----------] 9 tests from GraphConstruction (2657 ms total) 2: 2: [----------] 4 tests from Io 2: [ RUN ] Io.Order 2: 0:00:04.970 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:04.970 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:04.995 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:05.000 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: [ OK ] Io.Order (29 ms) 2: [ RUN ] Io.PairedInfo 2: [ OK ] Io.PairedInfo (2 ms) 2: [ RUN ] Io.KmerMapper 2: [ OK ] Io.KmerMapper (0 ms) 2: [ RUN ] Io.GFADBG 2: 0:00:05.002 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:05.002 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:05.002 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from src/test/debruijn/graph_fragments/tipobulge/tipobulge.grp 2: 0:00:05.002 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from src/test/debruijn/graph_fragments/tipobulge/tipobulge started 2: 0:00:05.002 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from src/test/debruijn/graph_fragments/tipobulge/tipobulge 2: 0:00:05.002 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:05.002 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:05.003 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:05.003 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:05.003 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from src/test/debruijn/graph_fragments/topology_ec/self_comp.grp 2: 0:00:05.003 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from src/test/debruijn/graph_fragments/topology_ec/self_comp started 2: 0:00:05.003 49M / 159M INFO General (graphio.cpp : 139) Reading coverage from src/test/debruijn/graph_fragments/topology_ec/self_comp 2: 0:00:05.005 49M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:05.005 49M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: [ OK ] Io.GFADBG (5 ms) 2: [----------] 4 tests from Io (37 ms total) 2: 2: [----------] 8 tests from PathExtend 2: [ RUN ] PathExtend.BidirectionalPathConstructor 2: 0:00:05.008 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:05.015 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:05.016 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp 2: 0:00:05.016 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:05.016 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathConstructor (8 ms) 2: [ RUN ] PathExtend.BidirectionalPathAddRemove 2: 0:00:05.016 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:05.016 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:05.016 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp 2: 0:00:05.016 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:05.016 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathAddRemove (0 ms) 2: [ RUN ] PathExtend.BidirectionalPathAddRemoveGaps 2: 0:00:05.016 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:05.016 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:05.016 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp 2: 0:00:05.016 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:05.016 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathAddRemoveGaps (0 ms) 2: [ RUN ] PathExtend.BidirectionalPathEquals 2: 0:00:05.016 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:05.016 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:05.016 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp 2: 0:00:05.016 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:05.016 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathEquals (0 ms) 2: [ RUN ] PathExtend.BidirectionalPathSubpaths 2: 0:00:05.016 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:05.016 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:05.016 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp 2: 0:00:05.016 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:05.016 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathSubpaths (0 ms) 2: [ RUN ] PathExtend.BidirectionalPathAddRemoveConjugate 2: 0:00:05.016 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:05.016 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:05.016 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp 2: 0:00:05.016 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:05.016 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathAddRemoveConjugate (0 ms) 2: [ RUN ] PathExtend.BidirectionalPathSearch 2: 0:00:05.016 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:05.016 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:05.017 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp 2: 0:00:05.017 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:05.017 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathSearch (0 ms) 2: [ RUN ] PathExtend.BidirectionalPathLoopDetector 2: 0:00:05.017 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:05.017 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:05.017 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp 2: 0:00:05.017 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:05.017 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathLoopDetector (0 ms) 2: [----------] 8 tests from PathExtend (9 ms total) 2: 2: [----------] 23 tests from OverlapRemoval 2: [ RUN ] OverlapRemoval.BasicNoDiff 2: 0:00:05.017 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:05.017 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:05.017 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp 2: 0:00:05.017 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:05.017 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] OverlapRemoval.BasicNoDiff (0 ms) 2: [ RUN ] OverlapRemoval.BasicDiff 2: 0:00:05.017 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:05.017 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:05.017 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp 2: 0:00:05.017 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:05.017 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] OverlapRemoval.BasicDiff (0 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatConjugateEdges 2: 0:00:05.017 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:05.017 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:05.017 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp 2: 0:00:05.017 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:05.017 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: 0:00:05.017 1M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: [ OK ] OverlapRemoval.BasicRepeatConjugateEdges (0 ms) 2: [ RUN ] OverlapRemoval.BasicRepeat 2: 0:00:05.017 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:05.017 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:05.017 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:05.017 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:05.023 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:05.023 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: [ OK ] OverlapRemoval.BasicRepeat (5 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatUneven 2: 0:00:05.023 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:05.023 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:05.023 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:05.023 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:05.027 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:05.032 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: [ OK ] OverlapRemoval.BasicRepeatUneven (12 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatAllDisconnected 2: 0:00:05.036 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:05.036 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:05.036 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:05.036 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:05.039 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:05.039 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: 0:00:05.039 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps 2: [ OK ] OverlapRemoval.BasicRepeatAllDisconnected (3 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatNoEffect 2: 0:00:05.039 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:05.039 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:05.048 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:05.052 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:05.055 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:05.055 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: [ OK ] OverlapRemoval.BasicRepeatNoEffect (15 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatEnd 2: 0:00:05.055 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:05.055 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:05.055 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:05.055 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:05.059 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:05.064 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: 0:00:05.068 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps 2: [ OK ] OverlapRemoval.BasicRepeatEnd (12 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatEndRetain 2: 0:00:05.068 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:05.068 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:05.068 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:05.068 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:05.071 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:05.071 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: 0:00:05.071 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps 2: [ OK ] OverlapRemoval.BasicRepeatEndRetain (4 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatStart 2: 0:00:05.072 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:05.079 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:05.080 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:05.080 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:05.083 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:05.083 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: 0:00:05.083 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps 2: [ OK ] OverlapRemoval.BasicRepeatStart (11 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatStartRetain 2: 0:00:05.083 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:05.083 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:05.083 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:05.083 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:05.087 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:05.092 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: 0:00:05.096 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps 2: [ OK ] OverlapRemoval.BasicRepeatStartRetain (12 ms) 2: [ RUN ] OverlapRemoval.BasicDeduplication 2: 0:00:05.096 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:05.096 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:05.096 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:05.096 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:05.099 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] OverlapRemoval.BasicDeduplication (3 ms) 2: [ RUN ] OverlapRemoval.BasicDeduplicationEqual 2: 0:00:05.100 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:05.108 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:05.112 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:05.112 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:05.115 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] OverlapRemoval.BasicDeduplicationEqual (15 ms) 2: [ RUN ] OverlapRemoval.DeduplicateDiff 2: 0:00:05.115 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:05.115 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:05.115 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:05.115 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:05.119 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] OverlapRemoval.DeduplicateDiff (8 ms) 2: [ RUN ] OverlapRemoval.DeduplicateDiffGap 2: 0:00:05.124 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:05.131 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:05.132 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:05.132 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:05.135 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] OverlapRemoval.DeduplicateDiffGap (11 ms) 2: [ RUN ] OverlapRemoval.DeduplicateMinEdgeLen1 2: 0:00:05.135 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:05.135 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:05.135 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:05.135 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:05.139 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] OverlapRemoval.DeduplicateMinEdgeLen1 (8 ms) 2: [ RUN ] OverlapRemoval.DeduplicateMinEdgeLen2 2: 0:00:05.144 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:05.148 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:05.148 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:05.148 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:05.151 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] OverlapRemoval.DeduplicateMinEdgeLen2 (7 ms) 2: [ RUN ] OverlapRemoval.EndEndMinEdgeLen 2: 0:00:05.151 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:05.151 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:05.151 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:05.151 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:05.155 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:05.160 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: 0:00:05.164 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps 2: [ OK ] OverlapRemoval.EndEndMinEdgeLen (12 ms) 2: [ RUN ] OverlapRemoval.Tricky0 2: 0:00:05.164 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:05.164 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:05.164 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:05.164 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:05.167 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:05.167 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: 0:00:05.167 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps 2: [ OK ] OverlapRemoval.Tricky0 (4 ms) 2: [ RUN ] OverlapRemoval.Tricky1 2: 0:00:05.168 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:05.175 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:05.180 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:05.180 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:05.183 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:05.183 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: 0:00:05.183 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps 2: [ OK ] OverlapRemoval.Tricky1 (15 ms) 2: [ RUN ] OverlapRemoval.Tricky2 2: 0:00:05.183 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:05.183 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:05.183 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:05.183 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:05.187 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:05.192 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: 0:00:05.196 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps 2: [ OK ] OverlapRemoval.Tricky2 (12 ms) 2: [ RUN ] OverlapRemoval.BasicMinEdgeLen 2: 0:00:05.196 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:05.196 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:05.196 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:05.196 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:05.199 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:05.199 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: 0:00:05.199 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps 2: [ OK ] OverlapRemoval.BasicMinEdgeLen (4 ms) 2: [ RUN ] OverlapRemoval.OverlapWithMiddle 2: 0:00:05.200 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:05.207 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:05.212 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:05.212 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:05.215 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:05.215 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: 0:00:05.215 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps 2: [ OK ] OverlapRemoval.OverlapWithMiddle (15 ms) 2: [----------] 23 tests from OverlapRemoval (198 ms total) 2: 2: [----------] 5 tests from GraphAligner 2: [ RUN ] GraphAligner.EdlibSHWFULLTest 2: 0:00:05.215 1M / 159M INFO General (graph_alignment_test.cpp : 31) Edlib: Result status = 0 2: [ OK ] GraphAligner.EdlibSHWFULLTest (0 ms) 2: [ RUN ] GraphAligner.EdlibSHWFULLTestZero 2: 0:00:05.215 1M / 159M INFO General (graph_alignment_test.cpp : 61) Edlib: Result status = 0 2: 0:00:05.215 1M / 159M INFO General (graph_alignment_test.cpp : 63) Edlib: Result ed = -1 2: [ OK ] GraphAligner.EdlibSHWFULLTestZero (8 ms) 2: [ RUN ] GraphAligner.TrivialTest 2: 0:00:05.223 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:05.228 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:05.228 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:05.228 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:05.231 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:05.231 4M / 159M INFO BWAIndex (bwa_index.cpp : 52) Setting BWA alignment mode to 'pacbio' 2: 0:00:05.234 5M / 159M INFO General (bwa_index.cpp : 150) Using BWA IS algorithm 2: [ OK ] GraphAligner.TrivialTest (330 ms) 2: [ RUN ] GraphAligner.DijkstraOneEdgeTest 2: 0:00:05.554 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:05.556 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:05.556 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:05.556 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:05.559 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] GraphAligner.DijkstraOneEdgeTest (6 ms) 2: [ RUN ] GraphAligner.DijkstraGrowEndsTest 2: 0:00:05.560 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:05.560 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:05.560 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:05.560 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:05.564 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] GraphAligner.DijkstraGrowEndsTest (11 ms) 2: [----------] 5 tests from GraphAligner (356 ms total) 2: 2: [----------] 1 test from VariableOverlaps 2: [ RUN ] VariableOverlaps.BasicOperations 2: 0:00:05.572 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:05.572 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:05.572 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:05.572 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: [ OK ] VariableOverlaps.BasicOperations (0 ms) 2: [----------] 1 test from VariableOverlaps (0 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 100 tests from 11 test suites ran. (5572 ms total) 2: [ PASSED ] 100 tests. 2/2 Test #2: debruijn_test .................... Passed 5.58 sec 100% tests passed, 0 tests failed out of 2 Total Test time (real) = 5.77 sec make[1]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=src -O--buildsystem=cmake dh_prep -O--sourcedirectory=src -O--buildsystem=cmake dh_auto_install --destdir=debian/spades/ -O--sourcedirectory=src -O--buildsystem=cmake cd obj-x86_64-linux-gnu && make -j12 install DESTDIR=/build/reproducible-path/spades-4.0.0\+dfsg1/debian/spades AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/spades-4.0.0+dfsg1/src -B/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades-bwa -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades-corrector-core -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/corrector -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/corrector/corrector.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades-hammer -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/hammer -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/hammer/config.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades-ionhammer -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/ionhammer -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/ionhammer/ionhammer.cfg -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades-core -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/rna_mode.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/detail_info_printer.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/mda_mode.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/meta_mode.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/toy.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/metaviral_mode.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/pe_params.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/config.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/sewage_mode.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/careful_mode.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/distance_estimation.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/isolate_mode.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/simplification.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/careful_mda_mode.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/hmm_mode.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/plasmid_mode.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/construction.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/metaplasmid_mode.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/large_genome_mode.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/rnaviral_mode.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/biosynthetic_spades_hmms -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/biosynthetic_spades_hmms/TE.hmm.gz -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/biosynthetic_spades_hmms/CStart.hmm.gz -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/biosynthetic_spades_hmms/KS.hmm.gz -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/biosynthetic_spades_hmms/AT.hmm.gz -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/biosynthetic_spades_hmms/KR.hmm.gz -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/biosynthetic_spades_hmms/AMP.hmm.gz -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/coronaspades_hmms -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/coronaspades_hmms/Phan-CoV.hmm.gz -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/coronaspades_hmms/Pfam-A.SARS-CoV-2.hmm.gz -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/sewage -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/sewage/usher_barcodes.csv -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/metaspades.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/plasmidspades.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/rnaspades.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/metaviralspades.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/metaplasmidspades.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/rnaviralspades.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/coronaspades.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades_init.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/process_cfg.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/scaffold_correction_stage.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/pipeline.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/error_correction_stage.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/spades_stage.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/check_test_stage.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/preprocess_reads_stage.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/stage.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/correction_stage.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/__init__.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/breaking_scaffolds_stage.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/terminating_stage.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/spades_iteration_stage.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/before_start_stage.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/common -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/common/SeqIO.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/common/sam_parser.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/common/alignment.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/common/__init__.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/common/parallel_launcher.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/executors -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/executors/executor_local.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/executors/executor_save_yaml.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/executors/executors.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/support.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/commands_parser.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/options_storage.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/scripts -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/scripts/copy_files.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/scripts/plasmid_glue.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/scripts/preprocess_contigs.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/scripts/preprocess_interlaced_reads.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/scripts/correction_iteration_script.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/scripts/breaking_scaffolds_script.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/scripts/check_test_script.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/scripts/compress_all.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/options_parser.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset/genes_1K.gff -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset/reference_1K.fa.gz -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset/ecoli_1K_1.fq.gz -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset/genes_1K.txt -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset/operons_1K.gff -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset/operons_1K.txt -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset/ecoli_1K_2.fq.gz -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset_plasmid -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset_plasmid/pl1.fq.gz -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset_plasmid/pl2.fq.gz -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades-convert-bin-to-fasta -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades-gbuilder -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades-gmapper -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades-gsimplifier -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades-kmercount -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades-read-filter -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades-kmer-estimating -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades-gfa-split -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/VERSION -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/README.md -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/LICENSE -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/GPLv2.txt make[1]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' debian/rules execute_after_dh_auto_install make[1]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1' # Use Debian-packaged yaml module find debian/spades \ -type f \ -exec sed -i 's/pyyaml[2|3]/yaml/' {} + mkdir -p debian/spades/usr/libexec/spades/ mv debian/spades/usr/bin/* debian/spades/usr/libexec/spades/ rm -f debian/spades/usr/share/spades/*.html rm -f debian/spades/usr/share/spades/manual.md rm -f debian/spades/usr/share/spades/GPLv2.txt rm -f debian/spades/usr/share/spades/README.md rm -f debian/spades/usr/share/spades/LICENSE make[1]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1' dh_install -O--sourcedirectory=src -O--buildsystem=cmake dh_installdocs -O--sourcedirectory=src -O--buildsystem=cmake dh_installchangelogs -O--sourcedirectory=src -O--buildsystem=cmake dh_installexamples -O--sourcedirectory=src -O--buildsystem=cmake debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1' mkdir -p /build/reproducible-path/spades-4.0.0+dfsg1/debian/man asciidoctor -a docdate='' -b manpage /build/reproducible-path/spades-4.0.0+dfsg1/debian/man_src/*.adoc cp /build/reproducible-path/spades-4.0.0+dfsg1/debian/man_src/*.? /build/reproducible-path/spades-4.0.0+dfsg1/debian/man dh_installman make[1]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1' dh_python3 -O--sourcedirectory=src -O--buildsystem=cmake dh_installsystemduser -O--sourcedirectory=src -O--buildsystem=cmake dh_lintian -O--sourcedirectory=src -O--buildsystem=cmake dh_perl -O--sourcedirectory=src -O--buildsystem=cmake dh_link -O--sourcedirectory=src -O--buildsystem=cmake dh_strip_nondeterminism -O--sourcedirectory=src -O--buildsystem=cmake dh_compress -O--sourcedirectory=src -O--buildsystem=cmake dh_fixperms -O--sourcedirectory=src -O--buildsystem=cmake dh_missing -O--sourcedirectory=src -O--buildsystem=cmake dh_dwz -a -O--sourcedirectory=src -O--buildsystem=cmake dh_strip -a -O--sourcedirectory=src -O--buildsystem=cmake dh_makeshlibs -a -O--sourcedirectory=src -O--buildsystem=cmake dh_shlibdeps -a -O--sourcedirectory=src -O--buildsystem=cmake dh_installdeb -O--sourcedirectory=src -O--buildsystem=cmake dh_gencontrol -O--sourcedirectory=src -O--buildsystem=cmake dh_md5sums -O--sourcedirectory=src -O--buildsystem=cmake dh_builddeb -O--sourcedirectory=src -O--buildsystem=cmake dpkg-deb: building package 'spades' in '../spades_4.0.0+dfsg1-2_amd64.deb'. dpkg-deb: building package 'spades-dbgsym' in '../spades-dbgsym_4.0.0+dfsg1-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../spades_4.0.0+dfsg1-2_amd64.buildinfo dpkg-genchanges --build=binary -O../spades_4.0.0+dfsg1-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3120234 and its subdirectories I: Current time: Fri Mar 14 21:47:25 -12 2025 I: pbuilder-time-stamp: 1742032045 Sat Mar 15 09:47:28 UTC 2025 I: 1st build successful. Starting 2nd build on remote node infom02-amd64.debian.net. Sat Mar 15 09:47:28 UTC 2025 I: Preparing to do remote build '2' on infom02-amd64.debian.net. Sat Mar 15 10:00:29 UTC 2025 I: Deleting $TMPDIR on infom02-amd64.debian.net. Sat Mar 15 10:00:29 UTC 2025 I: spades_4.0.0+dfsg1-2_amd64.changes: Format: 1.8 Date: Sun, 16 Feb 2025 11:28:59 +0100 Source: spades Binary: spades spades-dbgsym Architecture: amd64 Version: 4.0.0+dfsg1-2 Distribution: unstable Urgency: low Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: spades - genome assembler for single-cell and isolates data sets Changes: spades (4.0.0+dfsg1-2) unstable; urgency=low . Remove listed license files (ext/src/hmmer/libdivsufsort/COPYING) from copyright. Checksums-Sha1: 2b732c188dce0311c163ea4e27d4b17c9773e110 170196940 spades-dbgsym_4.0.0+dfsg1-2_amd64.deb 13324f91aa9ce7f4877dc0e57ce882c7eefd3ae7 10707 spades_4.0.0+dfsg1-2_amd64.buildinfo c1120a4a3baed995460ae59fc4c97cb8e509b71b 8066952 spades_4.0.0+dfsg1-2_amd64.deb Checksums-Sha256: 1f489f8952e47ad095cb67a95516ada3d44adfc866ce7080b179ea5457afb96a 170196940 spades-dbgsym_4.0.0+dfsg1-2_amd64.deb 0d15fb0b5ffa4bf6ed4a88d2020f56861503ce0a4c755fd02ca00dfc6e8a6388 10707 spades_4.0.0+dfsg1-2_amd64.buildinfo 8c57ebb467c002d249b719942e2e1b92db533d052c94203a7b3d25c63eb2f199 8066952 spades_4.0.0+dfsg1-2_amd64.deb Files: 29d3bf511e1c5fd838391c54899b6d6a 170196940 debug optional spades-dbgsym_4.0.0+dfsg1-2_amd64.deb 991ca5aaea78d62d31f013b38d1b78b3 10707 science optional spades_4.0.0+dfsg1-2_amd64.buildinfo 813e0151b3eea50140586a2cc757f508 8066952 science optional spades_4.0.0+dfsg1-2_amd64.deb Sat Mar 15 10:00:31 UTC 2025 I: diffoscope 289 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_33-52944.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.EDGLKHX8/spades_4.0.0+dfsg1-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.EDGLKHX8/spades_4.0.0+dfsg1-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.EDGLKHX8/spades_4.0.0+dfsg1-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.EDGLKHX8/b1/spades_4.0.0+dfsg1-2_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.EDGLKHX8/b2/spades_4.0.0+dfsg1-2_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.004s) 0.004s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 248ms CPU time consumed: 249ms Sat Mar 15 10:00:33 UTC 2025 I: diffoscope 289 found no differences in the changes files, and a .buildinfo file also exists. Sat Mar 15 10:00:33 UTC 2025 I: spades from unstable built successfully and reproducibly on amd64. Sat Mar 15 10:00:35 UTC 2025 I: Submitting .buildinfo files to external archives: Sat Mar 15 10:00:35 UTC 2025 I: Submitting 12K b1/spades_4.0.0+dfsg1-2_amd64.buildinfo.asc Sat Mar 15 10:00:36 UTC 2025 I: Submitting 12K b2/spades_4.0.0+dfsg1-2_amd64.buildinfo.asc Sat Mar 15 10:00:37 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat Mar 15 10:00:37 UTC 2025 I: Done submitting .buildinfo files. Sat Mar 15 10:00:37 UTC 2025 I: Removing signed spades_4.0.0+dfsg1-2_amd64.buildinfo.asc files: removed './b1/spades_4.0.0+dfsg1-2_amd64.buildinfo.asc' removed './b2/spades_4.0.0+dfsg1-2_amd64.buildinfo.asc'